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Recent Articles in Journal of Medical Internet Research

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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]

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]

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]

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

Zimmerman RK, Wolfe RM, Fox DE, Fox JR, Nowalk MP, Troy JA, Sharp LK
Vaccine criticism on the World Wide Web.
J Med Internet Res. 2005;7(2):e17.
BACKGROUND: The incidence of vaccine-preventable diseases is directly related to the number of unvaccinated children. Parents who refuse vaccination of their children frequently express concerns about vaccine safety. The Internet can influence perceptions about vaccines because it is the fastest growing source of consumer health information. However, few studies have analyzed vaccine criticism on the Web. OBJECTIVE: The purposes of this paper are to examine vaccine criticism on the Internet and to analyze the websites in order to identify common characteristics and ethical allegations. METHODS: A structured Web search was conducted for the terms "vaccine," "vaccination," "vaccinate," and "anti-vaccination" using a metasearch program that incorporated 8 search engines. This yielded 1138 Web pages representing 750 sites. Two researchers reviewed the sites for inclusion/exclusion criteria, resulting in 78 vaccine-critical sites, which were then abstracted for design, content, and allegations. RESULTS: The most common characteristic of vaccine-critical websites was the inclusion of statements linking vaccinations with specific adverse reactions, especially idiopathic chronic diseases such as multiple sclerosis, autism, and diabetes. Other common attributes (> or = 70% of websites) were links to other vaccine-critical websites; charges that vaccines contain contaminants, mercury, or "hot lots" that cause adverse events; claims that vaccines provide only temporary protection and that the diseases prevented are mild; appeals for responsible parenting through education and resisting the establishment; allegations of conspiracies and cover-ups to hide the truth about vaccine safety; and charges that civil liberties are violated through mandatory vaccination. CONCLUSIONS: Vaccine-critical websites frequently make serious allegations. With the burgeoning of the Internet as a health information source, an undiscerning or incompletely educated public may accept these claims and refuse vaccination of their children. As this occurs, the incidence of vaccine-preventable diseases can be expected to rise. [Abstract/Link to Full Text]

Clarke G, Eubanks D, Reid E, Kelleher C, O'Connor E, DeBar LL, Lynch F, Nunley S, Gullion C
Overcoming Depression on the Internet (ODIN) (2): a randomized trial of a self-help depression skills program with reminders.
J Med Internet Res. 2005;7(2):e16.
BACKGROUND: Guided self-help programs for depression (with associated therapist contact) have been successfully delivered over the Internet. However, previous trials of pure self-help Internet programs for depression (without therapist contact), including an earlier trial conducted by us, have failed to yield positive results. We hypothesized that methods to increase participant usage of the intervention, such as postcard or telephone reminders, might result in significant effects on depression. OBJECTIVES: This paper presents a second randomized trial of a pure self-help Internet site, ODIN (Overcoming Depression on the InterNet), for adults with self-reported depression. We hypothesized that frequently reminded participants receiving the Internet program would report greater reduction in depression symptoms and greater improvements in mental and physical health functioning than a comparison group with usual treatment and no access to ODIN. METHODS: This was a three-arm randomized control trial with a usual treatment control group and two ODIN intervention groups receiving reminders through postcards or brief telephone calls. The setting was a nonprofit health maintenance organization (HMO). We mailed recruitment brochures by US post to two groups: adults (n = 6030) who received depression medication or psychotherapy in the previous 30 days, and an age- and gender-matched group of adults (n = 6021) who did not receive such services. At enrollment and at 5-, 10- and 16-weeks follow-up, participants were reminded by email (and telephone, if nonresponsive) to complete online versions of the Center for Epidemiological Studies Depression Scale (CES-D) and the Short Form 12 (SF-12). We also recorded participant HMO health care services utilization in the 12 months following study enrollment. RESULTS: Out of a recruitment pool of 12051 approached subjects, 255 persons accessed the Internet enrollment site, completed the online consent form, and were randomized to one of the three groups: (1) treatment as usual control group without access to the ODIN website (n = 100), (2) ODIN program group with postcard reminders (n = 75), and (3) ODIN program group with telephone reminders (n = 80). Across all groups, follow-up completion rates were 64% (n = 164) at 5 weeks, 68% (n = 173) at 10 weeks, and 66% (n = 169) at 16 weeks. In an intention-to-treat analysis, intervention participants reported greater reductions in depression compared to the control group (P = .03; effect size = 0.277 standard deviation units). A more pronounced effect was detected among participants who were more severely depressed at baseline (P = .02; effect size = 0.537 standard deviation units). By the end of the study, 20% more intervention participants moved from the disordered to normal range on the CES-D. We found no difference between the two intervention groups with different reminders in outcomes measures or in frequency of log-ons. We also found no significant intervention effects on the SF-12 or health care services. CONCLUSIONS: In contrast to our earlier trial, in which participants were not reminded to use ODIN, in this trial we found a positive effect of the ODIN intervention compared to the control group. Future studies should address limitations of this trial, including relatively low enrollment and follow-up completion rates, and a restricted number of outcome measures. However, the low incremental costs of delivering this Internet program makes it feasible to offer this type of program to large populations with widespread Internet access. [Abstract/Link to Full Text]

Tjora A, Tran T, Faxvaag A
Privacy vs usability: a qualitative exploration of patients' experiences with secure Internet communication with their general practitioner.
J Med Internet Res. 2005;7(2):e15.
BACKGROUND: Direct electronic communication between patients and physicians has the potential to empower patients and improve health care services. Communication by regular email is, however, considered a security threat in many countries and is not recommended. Systems which offer secure communication have now emerged. Unlike regular email, secure systems require that users authenticate themselves. However, the authentication steps per se may become barriers that reduce use. OBJECTIVES: The objective was to study the experiences of patients who were using a secure electronic communication system. The focus of the study was the users' privacy versus the usability of the system. METHODS: Qualitative interviews were conducted with 15 patients who used a secure communication system (MedAxess) to exchange personal health information with their primary care physician. RESULTS: Six main themes were identified from the interviews: (1) supporting simple questions, (2) security issues, (3) aspects of written communication, (4) trust in the physician, (5) simplicity of MedAxess, and (6) trouble using the system. By using the system, about half of the patients (8/15) experienced easier access to their physician, with whom they tended to solve minor health problems and elaborate on more complex illness experiences. Two thirds of the respondents (10/15) found that their physician quickly responded to their MedAxess requests. As a result of the security barriers, the users felt that the system was secure. However, due to the same barriers, the patients considered the log-in procedure cumbersome, which had considerable negative impact on the actual use of the system. CONCLUSIONS: Despite a perceived need for secure electronic patient-physician communication systems, security barriers may diminish their overall usefulness. A dual approach is necessary to improve this situation: patients need to be better informed about security issues, and, at the same time, their experiences of using secure systems must be studied and used to improve user interfaces. [Abstract/Link to Full Text]

Simmons C, Nyhof-Young J, Bradley J
Shoestring budgets, band-AIDS, and team work: challenges and motivators in the development of a Web-based resource for undergraduate clinical skills teaching.
J Med Internet Res. 2005;7(2):e14.
BACKGROUND: Learning how to conduct a medical interview and perform a physical examination is fundamental to the practice of medicine; however, when this project began, the methods used to teach these skills to medical students at the University of Toronto (U of T) had not changed significantly since the early 1990s despite increasing outpatient care, shorter hospital stays, and heavy preceptor workloads. In response, a Web-based clinical skills resource was developed for the first-year undergraduate medical course-The Art and Science of Clinical Medicine I (ASCM I). OBJECTIVES: This paper examines our experiences with the development of the ASCM I website and details the challenges and motivators inherent in the production of a Web-based, multimedia medical education tool at a large Canadian medical school. METHODS: Interviews and a focus group were conducted with the development team to discover the factors that positively and negatively affected the development process. RESULTS: Motivating factors included team attributes such as strong leadership and judicious use of medical students and faculty volunteers as developers. Other motivators included a growing lack of instructional equivalency across diverse clinical teaching sites and financial and resource support by the Faculty of Medicine. Barriers to development included an administrative environment that did not yet fully incorporate information technology into its teaching vision and framework, a lack of academic incentive for faculty participation, and inadequate technical support, space, and equipment. CONCLUSIONS: The success of electronic educational resources such as the ASCM I website has caused a significant cultural shift within the Faculty of Medicine, resulting in the provision of more space, resources, and support for IT endeavours in the undergraduate medical curriculum. [Abstract/Link to Full Text]

Ross SE, Todd J, Moore LA, Beaty BL, Wittevrongel L, Lin CT
Expectations of patients and physicians regarding patient-accessible medical records.
J Med Internet Res. 2005;7(2):e13.
BACKGROUND: Middle class populations have supported shared medical records, including Internet-accessible medical records. The attitudes of lower income populations, and of physicians, are less clear. OBJECTIVES: The objective of this study was to compare the attitudes toward shared outpatient medical records among (1) socioeconomically disadvantaged patients in community health centers, (2) insured patients in primary care offices, and (3) a broad range of physicians in outpatient practice. METHODS: Written questionnaires were provided to patients in the waiting rooms of six primary care practices in the metropolitan Denver, Colorado area. Three practices were community health centers, and three practices were primary care clinics of an academic medical center. Questionnaires were also mailed to primary care physicians in the state of Colorado. RESULTS: There was a 79% response rate for patient surveys (601 surveys returned) and a 53% response rate for physician surveys (564 surveys returned). Academic medical center patients and community health center patients were equally likely to endorse shared medical records (94% vs 96%) and Internet-accessible records (54% vs 57%). Community health center patients were more likely than academic medical center patients to anticipate the benefits of shared medical records (mean number of expected benefits = 7.9 vs 7.1, P < .001), and they were also somewhat more likely to anticipate problems with shared records. Significant predictors of patient endorsement of Internet-accessible records were previous use of the Internet (OR = 2.45, CI 1.59-3.79), the number of expected benefits (OR = 1.12 per unit, CI 1.03-1.21), anticipation of asking more questions between visits (OR = 1.73, CI 1.18-2.54), and anticipation of finding the doctors' notes to be confusing (OR = 1.50, CI 1.01-2.22). Physicians were significantly more likely than patients to anticipate that access to records would cause problems. Physicians were significantly less likely than patients to anticipate benefits (mean number of expected benefits = 4.2 vs 7.5, P < .001). CONCLUSIONS: Interest in shared medical records is not confined to a white, middle class population. Shared medical records are almost universally endorsed across a broad range of ethnic and socioeconomic groups. A majority of patients are also interested in Internet-accessible records, but a substantial minority is not. The primary determinants of support of Internet-accessible records are not age, race, or education level; rather, they are previous experience with the Internet and patients' expectations of the benefits and drawbacks of reading their medical records. Physicians have more concerns about shared medical records and see less potential for benefit. The attitudes of patients and physicians may need to be reconciled for widespread adoption of shared medial records to be achieved. [Abstract/Link to Full Text]

Danaher BG, McKay HG, Seeley JR
The information architecture of behavior change websites.
J Med Internet Res. 2005;7(2):e12.
The extraordinary growth in Internet use offers researchers important new opportunities to identify and test new ways to deliver effective behavior change programs. The information architecture (IA)-the structure of website information--is an important but often overlooked factor to consider when adapting behavioral strategies developed in office-based settings for Web delivery. Using examples and relevant perspectives from multiple disciplines, we describe a continuum of website IA designs ranging from a matrix design to the tunnel design. The free-form matrix IA design allows users free rein to use multiple hyperlinks to explore available content according to their idiosyncratic interests. The more directive tunnel IA design (commonly used in e-learning courses) guides users step-by-step through a series of Web pages that are arranged in a particular order to improve the chances of achieving a goal that is measurable and consistent. Other IA designs are also discussed, including hierarchical IA and hybrid IA designs. In the hierarchical IA design, program content is arranged in a top-down manner, which helps the user find content of interest. The more complex hybrid IA design incorporates some combination of components that use matrix, tunnel, and/or hierarchical IA designs. Each of these IA designs is discussed in terms of usability, participant engagement, and program tailoring, as well as how they might best be matched with different behavior change goals (using Web-based smoking cessation interventions as examples). Our presentation underscores the role of considering and clearly reporting the use of IA designs when creating effective Web-based interventions. We also encourage the adoption of a multidisciplinary perspective as we move towards a more mature view of Internet intervention research. [Abstract/Link to Full Text]

Pagliari C, Sloan D, Gregor P, Sullivan F, Detmer D, Kahan JP, Oortwijn W, MacGillivray S
What is eHealth (4): a scoping exercise to map the field.
J Med Internet Res. 2005;7(1):e9.
BACKGROUND: Lack of consensus on the meaning of eHealth has led to uncertainty among academics, policymakers, providers and consumers. This project was commissioned in light of the rising profile of eHealth on the international policy agenda and the emerging UK National Programme for Information Technology (now called Connecting for Health) and related developments in the UK National Health Service. OBJECTIVES: To map the emergence and scope of eHealth as a topic and to identify its place within the wider health informatics field, as part of a larger review of research and expert analysis pertaining to current evidence, best practice and future trends. METHODS: Multiple databases of scientific abstracts were explored in a nonsystematic fashion to assess the presence of eHealth or conceptually related terms within their taxonomies, to identify journals in which articles explicitly referring to eHealth are contained and the topics covered, and to identify published definitions of the concept. The databases were Medline (PubMed), the Cumulative Index of Nursing and Allied Health Literature (CINAHL), the Science Citation Index (SCI), the Social Science Citation Index (SSCI), the Cochrane Database (including Dare, Central, NHS Economic Evaluation Database [NHS EED], Health Technology Assessment [HTA] database, NHS EED bibliographic) and ISTP (now known as ISI proceedings).We used the search query, "Ehealth OR e-health OR e*health". The timeframe searched was 1997-2003, although some analyses contain data emerging subsequent to this period. This was supplemented by iterative searches of Web-based sources, such as commercial and policy reports, research commissioning programmes and electronic news pages. Definitions extracted from both searches were thematically analyzed and compared in order to assess conceptual heterogeneity. RESULTS: The term eHealth only came into use in the year 2000, but has since become widely prevalent. The scope of the topic was not immediately discernable from that of the wider health informatics field, for which over 320000 publications are listed in Medline alone, and it is not explicitly represented within the existing Medical Subject Headings (MeSH) taxonomy. Applying eHealth as narrative search term to multiple databases yielded 387 relevant articles, distributed across 154 different journals, most commonly related to information technology and telemedicine, but extending to such areas as law. Most eHealth articles are represented on Medline. Definitions of eHealth vary with respect to the functions, stakeholders, contexts and theoretical issues targeted. Most encompass a broad range of medical informatics applications either specified (eg, decision support, consumer health information) or presented in more general terms (eg, to manage, arrange or deliver health care). However the majority emphasize the communicative functions of eHealth and specify the use of networked digital technologies, primarily the Internet, thus differentiating eHealth from the field of medical informatics. While some definitions explicitly target health professionals or patients, most encompass applications for all stakeholder groups. The nature of the scientific and broader literature pertaining to eHealth closely reflects these conceptualizations. CONCLUSIONS: We surmise that the field -- as it stands today -- may be characterized by the global definitions suggested by Eysenbach and Eng. [Abstract/Link to Full Text]

Wu RC, Delgado D, Costigan J, Maciver J, Ross H
Pilot study of an Internet patient-physician communication tool for heart failure disease management.
J Med Internet Res. 2005;7(1):e8.
BACKGROUND: Internet disease management has the promise of improving care in patients with heart failure but evidence supporting its use is limited. We have designed a Heart Failure Internet Communication Tool (HFICT), allowing patients to enter messages for clinicians, as well as their daily symptoms, weight, blood pressure and heart rate. Clinicians review the information on the same day and provide feedback. OBJECTIVE: This pilot study evaluated the feasibility and patients' acceptability of using the Internet to communicate with patients with symptomatic heart failure. METHODS: Patients with symptomatic heart failure were instructed how to use the Internet communication tool. The primary outcome measure was the proportion of patients who used the system regularly by entering information on average at least once per week for at least 3 months. Secondary outcomes measures included safety and maintainability of the tool. We also conducted a content analysis of a subset of the patient and clinician messages entered into the comments field. RESULTS: Between May 3, 1999 and November 1, 2002, 62 patients (mean age 48.7 years) were enrolled.. At 3 months 58 patients were alive and without a heart transplant. Of those, 26 patients (45%; 95% Confidence Interval, 0.33-0.58) continued using the system at 3 months. In 97% of all entries by participants weight was included; 68% of entries included blood pressure; and 71% of entries included heart rate. In 3386 entries out of all 5098 patient entries (66%), comments were entered. Functions that were not used included the tracking of diuretics, medications and treatment goals. The tool appeared to be safe and maintainable. Workload estimates for clinicians for entering a response to each patient's entry ranged from less than a minute to 5 minutes or longer for a detailed response. Patients sent 3386 comments to the Heart Function Clinic. Based on the content analysis of 100 patient entries, the following major categories of communication were identified: patient information; patient symptoms; patient questions regarding their condition; patient coordinating own care; social responses. The number of comments decreased over time for both patients and clinicians. CONCLUSION: While the majority of patients discontinued use, 45% of the patients used the system and continued to use it on average for 1.5 years. An Internet tool is a feasible method of communication in a substantial proportion of patients with heart failure. Further study is required to determine whether clinical outcomes, such as quality of life or frequency of hospitalization, are improved. [Abstract/Link to Full Text]

Farvolden P, Denisoff E, Selby P, Bagby RM, Rudy L
Usage and longitudinal effectiveness of a Web-based self-help cognitive behavioral therapy program for panic disorder.
J Med Internet Res. 2005;7(1):e7.
BACKGROUND: Anxiety disorders are common problems that result in enormous suffering and economic costs. The efficacy of Web-based self-help approaches for anxiety disorders has been demonstrated in a number of controlled trials. However, there is little data regarding the patterns of use and effectiveness of freely available Web-based interventions outside the context of controlled trials. OBJECTIVE: To examine the use and longitudinal effectiveness of a freely available, 12-session, Web-based, cognitive behavioral therapy (CBT) program for panic disorder and agoraphobia. METHODS: Cumulative anonymous data were analyzed from 99695 users of the Panic Center. Usage statistics for the website were examined and a longitudinal survey of self-reported symptoms for people who registered for the CBT program was conducted. The primary outcome measures were self-reported panic-attack frequency and severity at the beginning of each session (sessions 2-12). RESULTS: Between September 1, 2002 and February 1, 2004, there were 484695 visits and 1148097 page views from 99695 users to the Panic Center. In that same time period, 1161 users registered for the CBT program. There was an extremely high attrition rate with only 12 (1.03%) out of 1161 of registered users completing the 12-week program. However, even for those who remained in the program less than 12 weeks we found statistically significant reductions (P<.002) in self-reported panic attack frequency and severity, comparing 2 weeks of data against data after 3, 6, or 8 weeks. For example, the 152 users completing only 3 sessions of the program reduced their average number of attacks per day from 1.03 (week 2) to 0.63 (week 3) (P<.001). CONCLUSIONS: Freely available Web-based self-help will likely be associated with high attrition. However, for the highly self-selected group who stayed in the program, significant improvements were observed. [Abstract/Link to Full Text]

Koo M, Skinner H
Challenges of internet recruitment: a case study with disappointing results.
J Med Internet Res. 2005;7(1):e6.
BACKGROUND: The Internet provides tremendous opportunities for innovative research, but few publications on the use of the Internet for recruiting study participants exist. This paper summarizes our experiences from 2 studies in which we attempted to recruit teenagers on the Internet for a questionnaire study to evaluate a smoking-cessation website. OBJECTIVE: To evaluate strategies of recruiting teenagers for the evaluation of a smoking-cessation website through the Internet. METHODS: In Study 1 (Defined Community Recruitment), we sent invitation emails to registered members of a youth health website, CyberIsle. A total of 3801 email addresses were randomly divided into 2 groups. In the first group, emails indicated that the first 30 respondents would receive a Can dollars 20 electronic gift certificate for use at an online bookstore if they would go to the Smoking Zine website and respond to a short survey. For the second group, the email also indicated that respondents would receive an additional Can dollars 10 gift certificate if they referred their friends to the study. Reminder emails were sent 10 days after the sending of the initial invitation email. In Study 2 (Open Recruitment), we posted invitation messages on Web discussion boards, Usenet forums, and one specialized recruitment website, and attempted a snowball recruiting strategy. When potential participants arrived at the study site, they were automatically randomized into either the higher incentives group (Can dollars 15 electronic gift certificate) or lower incentive group (Can dollars 5 gift certificate). RESULTS: In Study 1 (defined community recruitment), 2109 emails were successfully delivered. Only 5 subjects (0.24%), including 1 referred by a friend, passed the recruitment process and completed the questionnaire; a further 6 individuals visited the information page of the study but did not complete the study. In Study 2 (open recruitment), the number of users seeing the advertisement is unknown. A total of 35 users arrived at the website, of whom 14 participants were recruited (8 from the Can dollars 15 gift certificate group and 6 from the Can dollars 5 gift certificate group). Another 5 were recruited from the general Internet community (3 from discussion boards and 2 from the Research Volunteers website). The remaining 9 participants were recruited through friend referrals with the snowball strategy. CONCLUSIONS: Overall, the recruitment rate was disappointingly low. In our case, recruitment using Internet technologies including email, electronic discussion boards, Usenet forums, and websites did not prove to be an effective approach for soliciting young subjects to participate in our research. Possible reasons are discussed, including the participants' perspective. A major challenge is to differentiate trustable and legitimate messages from spam and fraudulent misinformation on the Internet. From the researchers' perspective, approaches are needed to engage larger samples, to verify participants' attributes, and to evaluate and adjust for potential biases associated with Internet recruitment. [Abstract/Link to Full Text]

Paul J, Seib R, Prescott T
The Internet and clinical trials: background, online resources, examples and issues.
J Med Internet Res. 2005;7(1):e5.
Both the Internet and clinical trials were significant developments in the latter half of the twentieth century: the Internet revolutionized global communications and the randomized controlled trial provided a means to conduct an unbiased comparison of two or more treatments. Large multicenter trials are often burdened with an extensive development time and considerable expense, as well as significant challenges in obtaining, backing up and analyzing large amounts of data. Alongside the increasing complexities of the modern clinical trial has grown the power of the Internet to improve communications, centralize and secure data as well as to distribute information. As more and more clinical trials are required to coordinate multiple trial processes in real time, centers are turning to the Internet for the tools to manage the components of a clinical trial, either in whole or in part, to produce lower costs and faster results. This paper reviews the historical development of the Internet and the randomized controlled trial, describes the Internet resources available that can be used in a clinical trial, reviews some examples of online trials and describes the advantages and disadvantages of using the Internet to conduct a clinical trial. We also extract the characteristics of the 5 largest clinical trials conducted using the Internet to date, which together enrolled over 26000 patients. [Abstract/Link to Full Text]

Powell J, Buchan I
Electronic health records should support clinical research.
J Med Internet Res. 2005;7(1):e4.
One aspect of electronic care records which has received little attention is the potential benefit to clinical research. Electronic records could facilitate new interfaces between care and research environments, leading to great improvements in the scope and efficiency of research. Benefits range from systematically generating hypotheses for research to undertaking entire studies based only on electronic record data. Researchers and research managers must engage with electronic record initiatives to realize these benefits. Clinicians and patients must have confidence in the consent, confidentiality and security arrangements for the uses of secondary data. Provided that such initiatives establish adequate information governance arrangements, within a clear ethical framework, innovative clinical research should flourish. Major benefits to patient care could ensue given sufficient development of the care-research interface via electronic records. [Abstract/Link to Full Text]

Gunter TD, Terry NP
The emergence of national electronic health record architectures in the United States and Australia: models, costs, and questions.
J Med Internet Res. 2005;7(1):e3.
Emerging electronic health record models present numerous challenges to health care systems, physicians, and regulators. This article provides explanation of some of the reasons driving the development of the electronic health record, describes two national electronic health record models (currently developing in the United States and Australia) and one distributed, personal model. The US and Australian models are contrasted in their different architectures ("pull" versus "push") and their different approaches to patient autonomy, privacy, and confidentiality. The article also discusses some of the professional, practical, and legal challenges that health care providers potentially face both during and after electronic health record implementation. [Abstract/Link to Full Text]

Etter JF
Comparing the efficacy of two Internet-based, computer-tailored smoking cessation programs: a randomized trial.
J Med Internet Res. 2005;7(1):e2.
BACKGROUND: Online computer-tailored smoking cessation programs have not yet been compared directly. OBJECTIVE: To compare the efficacy of two Internet-based, computer-tailored smoking cessation programs. METHODS: Randomized controlled trial conducted in 2003-2004. Visitors to a smoking cessation website were randomly assigned to either an original online, interactive smoking cessation program or to a modified program. Both programs consisted of tailored, personalized counseling letters based on participants' characteristics, followed by monthly email reminders. The original program was based on psychological and addiction theory, and on preliminary research conducted in the same population. The modified program was shorter and contained more information on nicotine replacement therapy and nicotine dependence, and less information on health risks and coping strategies. In both programs, 1 month and 2 months after entering the study, participants were invited by email to answer the same tailoring questionnaire again in order to receive a second counseling letter. Participants in both programs obtained, on average, 1.2 feedback counseling letters over 2.5 months, and 84% received only 1 feedback letter. The outcome was self-reported smoking abstinence (no puff of tobacco in the previous 7 days), assessed 2.5 months after entry in the program. We report results from intention-to-treat (ITT) analyses, where all non-respondents at follow-up were counted as smokers. RESULTS: The baseline questionnaire was answered by a total of 11969 current (74%) and former (26%) smokers, and the follow-up survey by 4237 people (35%). In an ITT analysis, abstinence rates in baseline current smokers were respectively 10.9% and 8.9% (odds ratio [OR]=1.24, 95% confidence interval [CI]1.08-1.43, P=.003) in the original and modified programs, and 25.2% and 15.7% (OR=1.81, CI 1.51-2.16, P<.001) in baseline former smokers. While we found statistically significant differences in quit rates in smokers in the contemplation stage favoring the original program (OR=1.54, CI 1.18-2.02, P=.002), no between-group differences in quit rates were observed in smokers in the precontemplation (OR=1.07, CI 0.36-3.14, P=.91) and preparation (OR=1.15, CI 0.97-1.37, P=.10) stages of change. CONCLUSIONS: In smokers in the contemplation stage of change and in former smokers, the original program produced higher smoking abstinence rates than the modified program. [Abstract/Link to Full Text]

Eysenbach G
The law of attrition.
J Med Internet Res. 2005;7(1):e11.
In an ongoing effort of this Journal to develop and further the theories, models, and best practices around eHealth research, this paper argues for the need for a "science of attrition", that is, a need to develop models for discontinuation of eHealth applications and the related phenomenon of participants dropping out of eHealth trials. What I call "law of attrition" here is the observation that in any eHealth trial a substantial proportion of users drop out before completion or stop using the application. This feature of eHealth trials is a distinct characteristic compared to, for example, drug trials. The traditional clinical trial and evidence-based medicine paradigm stipulates that high dropout rates make trials less believable. Consequently eHealth researchers tend to gloss over high dropout rates, or not to publish their study results at all, as they see their studies as failures. However, for many eHealth trials, in particular those conducted on the Internet and in particular with self-help applications, high dropout rates may be a natural and typical feature. Usage metrics and determinants of attrition should be highlighted, measured, analyzed, and discussed. This also includes analyzing and reporting the characteristics of the subpopulation for which the application eventually "works", ie, those who stay in the trial and use it. For the question of what works and what does not, such attrition measures are as important to report as pure efficacy measures from intention-to-treat (ITT) analyses. In cases of high dropout rates efficacy measures underestimate the impact of an application on a population which continues to use it. Methods of analyzing attrition curves can be drawn from survival analysis methods, eg, the Kaplan-Meier analysis and proportional hazards regression analysis (Cox model). Measures to be reported include the relative risk of dropping out or of stopping the use of an application, as well as a "usage half-life", and prediction models reporting demographic usage discontinuation in a population. Differential dropout or usage rates between two interventions could be a standard metric for the "usability efficacy" of a system. A "run-in and withdrawal" trial design is suggested as a methodological innovation for Internet-based trials with a high number of initial dropouts/nonusers and a stable group of hardcore users. [Abstract/Link to Full Text]

Christensen H, Mackinnon A
The law of attrition revisited.
J Med Internet Res. 2006;8(3):e20; author reply e21. [Abstract/Link to Full Text]

Lasker JN, Sogolow ED, Sharim RR
The role of an online community for people with a rare disease: content analysis of messages posted on a primary biliary cirrhosis mailinglist.
J Med Internet Res. 2005;7(1):e10.
BACKGROUND: This study focuses on the role of an Internet-based group for people who have an autoimmune liver disease, primary biliary cirrhosis. Primary biliary cirrhosis is a relatively rare disease, affects primarily women in their 40's and older, and is not well understood. The PBCers Organization (PBC stands for primary biliary cirrhosis) provides electronic mailinglists (listservs) and informational resources for those with primary biliary cirrhosis. OBJECTIVES: (1) to identify the issues of greatest importance to those posting to the listserv, specifically the relative importance of biomedical, socioemotional, and organizational/systems messages; (2) to compare frequency and content of posts by people at different stages of disease; (3) to identify how people with primary biliary cirrhosis represent the psychosocial challenges and dilemmas (role and identity change, uncertainty, and stigma) identified in the social-scientific literature as key elements of the experience of chronic disease. METHODS: The paper is based on content analysis of messages posted during two months to the Daily Digest listserv for people who have primary biliary cirrhosis. To analyze the posts, we developed a coding system with three major categories--biomedical, socioemotional, and systems/organizations--and 12 codes in each category. RESULTS: A total of 275 people posted 710 messages. Of the 250 people for whom information on gender was available, 239 (95.6%) were women and 11 (4.4%) were men. Analysis of 710 messages posted to the listserv revealed a predominance of requests for and reports of biomedical information, such as health care providers (32.7%), medications (30.9%), tests and procedures (25.8%), and symptoms (25.7%), combined with very frequent expressions of emotional support. The most frequent single topics were peer support (included in 40.6% of all posts) and positive emotions (25.3%). Posters who reported fewer years since diagnosis were more likely to be seeking biomedical information than those who were further in time from their diagnosis (r= -.241, P<.001, n=313). Those in later stages posted an average of 3.87 messages, compared to an average of 2.64 for people in earlier stages (t= 1.786, P=.08, n=90), which is different from what we expected. No relation between years since diagnosis or age and number of messages was found. Contrary to our expectations, the topics reflecting issues of role change/identity (2.9%), stigma (0.7%), and thoughts about the future (3.9%), all identified in social-scientific literature as key concerns for people with chronic illness, appeared infrequently in this set of messages. CONCLUSIONS: Messages exchanged on this particular mailing list have a biomedical, rather than socioemotional or organizational, emphasis. The Internet offers a highly valued opportunity for those with rare diseases to connect with, learn from, and provide support to others having similar experiences. Research that compares those with primary biliary cirrhosis, who are involved in an Internet support group and those who are not, would be an important next step to better understanding the role of the Internet among patients with chronic liver disease and the implications of it in the course of their illness. [Abstract/Link to Full Text]

Oh H, Rizo C, Enkin M, Jadad A
What is eHealth (3): a systematic review of published definitions.
J Med Internet Res. 2005;7(1):e1.
CONTEXT: The term eHealth is widely used by many individuals, academic institutions, professional bodies, and funding organizations. It has become an accepted neologism despite the lack of an agreed-upon clear or precise definition. We believe that communication among the many individuals and organizations that use the term could be improved by comprehensive data about the range of meanings encompassed by the term. OBJECTIVE: To report the results of a systematic review of published, suggested, or proposed definitions of eHealth. DATA SOURCES: Using the search query string "eHealth" OR "e-Health" OR "electronic health", we searched the following databases: Medline and Premedline (1966-June 2004), EMBASE (1980-May 2004), International Pharmaceutical Abstracts (1970-May 2004), Web of Science (all years), Information Sciences Abstracts (1966-May 2004), Library Information Sciences Abstracts (1969-May 2004), and Wilson Business Abstracts (1982-March 2004). In addition, we searched dictionaries and an Internet search engine. STUDY SELECTION: We included any source published in either print format or on the Internet, available in English, and containing text that defines or attempts to define eHealth in explicit terms. Two of us independently reviewed titles and abstracts of citations identified in the bibliographic databases and Internet search, reaching consensus on relevance by discussion. DATA EXTRACTION: We retrieved relevant reports, articles, references, letters, and websites containing definitions of eHealth. Two of us qualitatively analyzed the definitions and coded them for content, emerging themes, patterns, and novel ideas. DATA SYNTHESIS: The 51 unique definitions that we retrieved showed a wide range of themes, but no clear consensus about the meaning of the term eHealth. We identified 2 universal themes (health and technology) and 6 less general (commerce, activities, stakeholders, outcomes, place, and perspectives). CONCLUSIONS: The widespread use of the term eHealth suggests that it is an important concept, and that there is a tacit understanding of its meaning. This compendium of proposed definitions may improve communication among the many individuals and organizations that use the term. [Abstract/Link to Full Text]

Norman C
CATCH-IT report: evaluation of an Internet-based smoking cessation program: lessons learned from a pilot study.
J Med Internet Res. 2004 Dec 31;6(4):e47; discussion e48. [Abstract/Link to Full Text]

Christensen H, Griffiths KM, Korten AE, Brittliffe K, Groves C
A comparison of changes in anxiety and depression symptoms of spontaneous users and trial participants of a cognitive behavior therapy website.
J Med Internet Res. 2004 Dec 22;6(4):e46.
BACKGROUND: In randomized controlled trials Internet sites have been shown to be effective in the treatment of depression and anxiety. However, it is unclear if the positive effects demonstrated in these trials transfer to community users of such sites. OBJECTIVE: To compare anxiety and depression outcomes for spontaneous visitors to a publicly accessible cognitive behavior therapy website (MoodGYM) (http://moodgym.anu.edu.au) with outcomes achieved through a randomized controlled efficacy trial of the same site. METHODS: All community visitors to the MoodGYM site between April 2001 and September 2003 were sampled: 182 participants in the BlueMood Trial who had been randomly assigned to the MoodGYM site as part of a large trial and 19607 visitors (public registrants) to the site. Symptom assessments (quizzes) were repeated within the website intervention to allow the examination of change in symptoms across modules. Outcome variables were (1) age, gender, initial depression severity scores, and number of assessments attempted, and (2) symptom change measures based on Goldberg anxiety and depression scores recorded on a least two occasions. RESULTS: Public registrants did not differ from trial participants in gender, age, or initial level of depression, which was high for both groups relative to previously published epidemiological data sets. Trial participants completed more assessments. No significant differences in anxiety or depression change scores were observed, with both public registrants and trial participants improving through the training program. CONCLUSIONS: Public registrants to a cognitive behavior therapy website show significant change in anxiety and depression symptoms. The extent of change does not differ from that exhibited by participants enrolled on the website for a randomized controlled trial. [Abstract/Link to Full Text]

Bello IS, Arogundade FA, Sanusi AA, Ezeoma IT, Abioye-Kuteyi EA, Akinsola A
Knowledge and utilization of Information Technology among health care professionals and students in Ile-Ife, Nigeria: a case study of a university teaching hospital.
J Med Internet Res. 2004 Dec 17;6(4):e45.
BACKGROUND: The computer revolution and Information Technology (IT) have transformed modern health care systems in the areas of communication, teaching, storage and retrieval of medical information. These developments have positively impacted patient management and the training and retraining of healthcare providers. Little information is available on the level of training and utilization of IT among health care professionals in developing countries. OBJECTIVES: To assess the knowledge and utilization pattern of information technology among health care professionals and medical students in a university teaching hospital in Nigeria. METHODS: Self-structured pretested questionnaires that probe into the knowledge, attitudes and utilization of computers and IT were administered to a randomly selected group of 180 health care professionals and medical students. Descriptive statistics on their knowledge, attitude and utilization patterns were calculated. RESULTS: A total of 148 participants (82%) responded, which included 60 medical students, 41 medical doctors and 47 health records staff. Their ages ranged between 22 and 54 years. Eighty respondents (54%) reportedly had received some form of computer training while the remaining 68 (46%) had no training. Only 39 respondents (26%) owned a computer while the remaining 109 (74%) had no computer. In spite of this a total of 28 respondents (18.9%) demonstrated a good knowledge of computers while 87 (58.8%) had average knowledge. Only 33 (22.3%) showed poor knowledge. Fifty-nine respondents (39.9%) demonstrated a good attitude and good utilization habits, while in 50 respondents (33.8%) attitude and utilization habits were average and in 39 (26.4%) they were poor. While 25% of students and 27% of doctors had good computer knowledge (P=.006), only 4.3% of the records officers demonstrated a good knowledge. Forty percent of the medical students, 54% of the doctors and 27.7% of the health records officers showed good utilization habits and attitudes (P=.01) CONCLUSION: Only 26% of the respondents possess a computer, and only a small percentage of the respondents demonstrated good knowledge of computers and IT, hence the suboptimal utilization pattern. The fact that the health records officers by virtue of their profession had better training opportunities did not translate into better knowledge and utilization habits, hence the need for a more structured training, one which would form part of the curriculum. This would likely have more impact on the target population than ad hoc arrangements. [Abstract/Link to Full Text]

Verheijden M, Bakx JC, Akkermans R, van den Hoogen H, Godwin NM, Rosser W, van Staveren W, van Weel C
Web-based targeted nutrition counselling and social support for patients at increased cardiovascular risk in general practice: randomized controlled trial.
J Med Internet Res. 2004 Dec 16;6(4):e44.
BACKGROUND: Using the Internet may prove useful in providing nutrition counselling and social support for patients with chronic diseases. OBJECTIVE: We evaluated the impact of Web-based nutrition counselling and social support on social support measures, anthropometry, blood pressure, and serum cholesterol in patients at increased cardiovascular risk. METHODS: We conducted a randomized controlled trial among patients with increased cardiovascular risk in Canadian family practices. During 8 months, patients in the intervention group and control groups received usual care. Patients in the intervention group also had access to a Web-based nutrition counselling and social support tool (Heartweb). Site use during the study was monitored. We measured social support, body mass index, waist/hip ratio, blood pressure, and cholesterol levels at baseline and at 4 and 8 months to assess the effectiveness of the intervention. RESULTS: We randomized 146 patients into the Web-based intervention (n=73) or the control group (n=73). Within the Web-based intervention group, Heartweb was used by only 33% (24/73) of patients, with users being significantly younger than nonusers (P=.03). There were no statistically significant differences between the intervention group and the control group in changes in social support, anthropometry, blood pressure, and serum cholesterol levels. CONCLUSIONS: Uptake of the Web-based intervention was low. This study showed no favourable effects of a Web-based nutrition counselling and social support intervention on social support, anthropometry, blood pressure, and serum cholesterol. Improvements in reach and frequency of site use are needed to increase the effectiveness of Web-based interventions. [Abstract/Link to Full Text]

Cohall AT, Cohall R, Dye B, Dini S, Vaughan RD
Parents of urban adolescents in Harlem, New York, and the Internet: a cross-sectional survey on preferred resources for health information.
J Med Internet Res. 2004 Dec 3;6(4):e43.
BACKGROUND: Vulnerable populations suffer disproportionately from a variety of health conditions. Access to health information is an important component of health promotion. Reports suggest that while health providers and print media are traditional sources of information, the Internet may be becoming an increasingly important resource for consumers. Particularly, for parents of urban adolescents of color, the Internet could prove to be a valuable asset in helping them understand adolescent health and behavioral issues. OBJECTIVE: To determine the types of adolescent health and behavioral issues of concern to parents of color and to assess their preference for sources of health information, including the Internet. METHODS: A confidential, self-administered survey was administered to parents (largely of African American and Hispanic descent) of 9th-grade students over a 2-year period during 2001-2002 in Harlem, NY. The instrument assessed health and behavioral topics of concern, preferred resources for information, ownership and utilization patterns of computers and the Internet, and interest in obtaining additional computer/Internet training. RESULTS: A total of 419 surveys were completed; 165 in 2001 (67% response rate) and 254 in 2002 (no response rate available). Analysis of responses indicated a substantial degree of interest in obtaining information about a variety of adolescent health issues, including: HIV, sexually transmitted infections, , mental health concerns and relationships with family and peers. While home ownership of computers (84%) and access to the Internet were reasonably high (74%), use of the Internet for health information was low (14%). However, 62% of parents indicated a strong desire to have more instruction on computers and the Internet. CONCLUSIONS: Compared to other sources of health information, the Internet is underutilized by urban parents of color. Additional research is needed to identify strategies to improve utilization and assess subsequent impact on parenting activities. [Abstract/Link to Full Text]

Anhøj J, Møldrup C
Feasibility of collecting diary data from asthma patients through mobile phones and SMS (short message service): response rate analysis and focus group evaluation from a pilot study.
J Med Internet Res. 2004 Dec 2;6(4):e42.
BACKGROUND: Self-management of asthma may improve asthma outcomes. The Internet has been suggested as a tool for the monitoring and self-management of asthma. However, in a recent study we found that a Web interface had some disadvantages and that users stopped using the application after a short while. OBJECTIVE: The primary objective of this study was to evaluate, from a user perspective, the feasibility of using short message service (SMS) for asthma diary data collection through mobile phones. The secondary objective was to investigate patient compliance with an SMS diary, as measured by response rates over time. METHODS: The study included quantitative response rate data, based on SMS collection, and qualitative data from a traditional focus group setting. In a period of 2 months, the participants received 4 SMS messages each day, including a medication reminder, a request to enter peak flow, data on sleep loss, and medication dosage. Participants were asked to reply to a minimum of 3 of the messages per day. Diary inputs were collected in a database and the response rate per patient was expressed as the number of diary inputs (SMS replies) divided by diary requests (product of number of days in the study and the number of diary questions per day) for each participant. After the study period, the participants were invited to a focus group interview addressing the participants' attitudes to their disease, their experience with the SMS asthma diary, and their future expectations from the SMS asthma diary. RESULTS: Twelve patients with asthma (6 males, 6 females) participated in the data collection study. The median age was 38.5 (range: 13-57) years. The median response rate per patient was 0.69 (range: 0.03-0.98), ie, half the participants reported more than about two thirds of the requested diary data. Furthermore, response rates were relatively steady during the study period with no signs of decreasing usage over time. From the subsequent focus group interview with 9 users we learned that, in general, the participants were enthusiastic about the SMS diary--it became an integrated part of their everyday life. However, the participants wished for a simpler diary with only one SMS message to respond to and a system with a Web interface for system customization and graphical display of diary data history. CONCLUSION: This study suggests that SMS collection of asthma diary data is feasible, and that SMS may be a tool for supporting the self-management of asthma (and possibly other chronic diseases) in motivated and self-efficacious patients because mobile phones are a part of people's everyday lives and enable active requests for data wherever the patient is. The combination of SMS data collection and a traditional Web page for data display and system customization may be a better and more usable tool for patients than the use of Web-based asthma diaries which suffer from high attrition rates. [Abstract/Link to Full Text]

Hirshfield S, Remien RH, Walavalkar I, Chiasson MA
Crystal methamphetamine use predicts incident STD infection among men who have sex with men recruited online: a nested case-control study.
J Med Internet Res. 2004 Nov 29;6(4):e41.
BACKGROUND: Among men who have sex with men (MSM), the number of newly diagnosed human immunodeficiency virus (HIV) infections has increased by approximately 60% since 1999. Factors that may be contributing to this resurgence include a widely reported increase in bacterial sexually transmitted diseases (STDs) among HIV-positive and HIV-negative MSM, as well as unsafe sexual practices. OBJECTIVE: This research was undertaken to learn more about risk behaviors associated with an incident STD among MSM. METHODS: A nested case-control study was conducted, using data from a cross-sectional Internet survey of MSM (N=2643), which investigated risk behaviors during a 6-month period in 2001. Chi-square and logistic regression methods were used to estimate the likelihood of acquiring an incident STD versus no STD. RESULTS: Eighty-five percent of the respondents were white, 46% were under age 30, and 80% had met sex partners online; 7% were HIV-positive. Men with an incident STD were more likely than men without an STD to report drug use (crystal methamphetamine odds ratio 3.8; 95% confidence interval 2.1-6.7; cocaine OR 2.3; 95% CI 1.2-4.2; ecstasy OR 2.2; 95% CI 1.3-3.8; Viagra OR 2.1; 95% CI 1.2-3.7), alcohol before or during sex (OR 1.9; 95% CI 1.2-2.9), and high-risk sexual behavior (unprotected anal intercourse OR 5.0; 95% CI 2.8-8.9; multiple sex partners OR 5.9; 95% CI 2.5-13.8). In the multivariate analysis, significant independent predictors associated with an incident STD were crystal methamphetamine use (adjusted OR 2.0; 95% CI 1.1-3.8), unprotected anal intercourse (adjusted OR 3.4; 95% CI 1.9-6.3), and 6 or more sex partners during the study period (adjusted OR 3.3; 95% CI 1.4-7.8). CONCLUSION: Identifying and treating MSM who have STDs, or who are at increased risk for acquiring STDs, is crucial in preventing the further spread of disease. In addition, there is a need to integrate HIV/STD and substance use prevention and education into Web-based and community-based venues. [Abstract/Link to Full Text]

Wantland DJ, Portillo CJ, Holzemer WL, Slaughter R, McGhee EM
The effectiveness of Web-based vs. non-Web-based interventions: a meta-analysis of behavioral change outcomes.
J Med Internet Res. 2004 Nov 10;6(4):e40.
BACKGROUND: A primary focus of self-care interventions for chronic illness is the encouragement of an individual's behavior change necessitating knowledge sharing, education, and understanding of the condition. The use of the Internet to deliver Web-based interventions to patients is increasing rapidly. In a 7-year period (1996 to 2003), there was a 12-fold increase in MEDLINE citations for "Web-based therapies." The use and effectiveness of Web-based interventions to encourage an individual's change in behavior compared to non-Web-based interventions have not been substantially reviewed. OBJECTIVE: This meta-analysis was undertaken to provide further information on patient/client knowledge and behavioral change outcomes after Web-based interventions as compared to outcomes seen after implementation of non-Web-based interventions. METHODS: The MEDLINE, CINAHL, Cochrane Library, EMBASE, ERIC, and PSYCHInfo databases were searched for relevant citations between the years 1996 and 2003. Identified articles were retrieved, reviewed, and assessed according to established criteria for quality and inclusion/exclusion in the study. Twenty-two articles were deemed appropriate for the study and selected for analysis. Effect sizes were calculated to ascertain a standardized difference between the intervention (Web-based) and control (non-Web-based) groups by applying the appropriate meta-analytic technique. Homogeneity analysis, forest plot review, and sensitivity analyses were performed to ascertain the comparability of the studies. RESULTS: Aggregation of participant data revealed a total of 11,754 participants (5,841 women and 5,729 men). The average age of participants was 41.5 years. In those studies reporting attrition rates, the average drop out rate was 21% for both the intervention and control groups. For the five Web-based studies that reported usage statistics, time spent/session/person ranged from 4.5 to 45 minutes. Session logons/person/week ranged from 2.6 logons/person over 32 weeks to 1008 logons/person over 36 weeks. The intervention designs included one-time Web-participant health outcome studies compared to non-Web participant health outcomes, self-paced interventions, and longitudinal, repeated measure intervention studies. Longitudinal studies ranged from 3 weeks to 78 weeks in duration. The effect sizes for the studied outcomes ranged from -.01 to .75. Broad variability in the focus of the studied outcomes precluded the calculation of an overall effect size for the compared outcome variables in the Web-based compared to the non-Web-based interventions. Homogeneity statistic estimation also revealed widely differing study parameters (Q(w16) = 49.993, P < or = .001). There was no significant difference between study length and effect size. Sixteen of the 17 studied effect outcomes revealed improved knowledge and/or improved behavioral outcomes for participants using the Web-based interventions. Five studies provided group information to compare the validity of Web-based vs. non-Web-based instruments using one-time cross-sectional studies. These studies revealed effect sizes ranging from -.25 to +.29. Homogeneity statistic estimation again revealed widely differing study parameters (Q(w4) = 18.238, P < or = .001). CONCLUSIONS: The effect size comparisons in the use of Web-based interventions compared to non-Web-based interventions showed an improvement in outcomes for individuals using Web-based interventions to achieve the specified knowledge and/or behavior change for the studied outcome variables. These outcomes included increased exercise time, increased knowledge of nutritional status, increased knowledge of asthma treatment, increased participation in healthcare, slower health decline, improved body shape perception, and 18-month weight loss maintenance. [Abstract/Link to Full Text]

Leece P, Bhandari M, Sprague S, Swiontkowski MF, Schemitsch EH, Tornetta P, Devereaux PJ, Guyatt GH
Internet versus mailed questionnaires: a controlled comparison (2).
J Med Internet Res. 2004 Oct 29;6(4):e39.
BACKGROUND: Low response rates among surgeons can threaten the validity of surveys. Internet technologies may reduce the time, effort, and financial resources needed to conduct surveys. OBJECTIVE: We investigated whether using Web-based technology could increase the response rates to an international survey. METHODS: We solicited opinions from the 442 surgeon-members of the Orthopaedic Trauma Association regarding the treatment of femoral neck fractures. We developed a self-administered questionnaire after conducting a literature review, focus groups, and key informant interviews, for which we used sampling to redundancy techniques. We administered an Internet version of the questionnaire on a Web site, as well as a paper version, which looked similar to the Internet version and which had identical content. Only those in our sample could access the Web site. We alternately assigned the participants to receive the survey by mail (n=221) or an email invitation to participate on the Internet (n=221). Non-respondents in the mail arm received up to three additional copies of the survey, while non-respondents in the Internet arm received up to three additional requests, including a final mailed copy. All participants in the Internet arm had an opportunity to request an emailed Portable Document Format (PDF) version. RESULTS: The Internet arm demonstrated a lower response rate (99/221, 45%) than the mail questionnaire arm (128/221, 58%) (absolute difference 13%, 95% confidence interval 4%-22%, P<0.01). CONCLUSIONS: Our Internet-based survey to surgeons resulted in a significantly lower response rate than a traditional mailed survey. Researchers should not assume that the widespread availability and potential ease of Internet-based surveys will translate into higher response rates. [Abstract/Link to Full Text]

Leece P, Bhandari M, Sprague S, Swiontkowski MF, Schemitsch EH, Tornetta P, Devereaux PJ, Guyatt GH
Internet versus mailed questionnaires: a randomized comparison (2).
J Med Internet Res. 2004 Sep 24;6(3):e30.
BACKGROUND: Low response rates among surgeons can threaten the validity of surveys. Internet technologies may reduce the time, effort, and financial resources needed to conduct surveys. OBJECTIVE: We investigated whether using Web-based technology could increase the response rates to an international survey. METHODS: We solicited opinions from the 442 surgeon-members of the Orthopaedic Trauma Association regarding the treatment of femoral neck fractures. We developed a self-administered questionnaire after conducting a literature review, focus groups, and key informant interviews, for which we used sampling to redundancy techniques. We administered an Internet version of the questionnaire on a Web site, as well as a paper version, which looked similar to the Internet version and which had identical content. Only those in our sample could access the Web site. We alternately assigned the participants to receive the survey by mail (n=221) or an email invitation to participate on the Internet (n=221). Non-respondents in the mail arm received up to three additional copies of the survey, while non-respondents in the Internet arm received up to three additional requests, including a final mailed copy. All participants in the Internet arm had an opportunity to request an emailed Portable Document Format (PDF) version. RESULTS: The Internet arm demonstrated a lower response rate (99/221, 45%) than the mail questionnaire arm (129/221, 58%) (absolute difference 13%, 95% confidence interval 4%-22%, P<0.01). CONCLUSIONS: Our Internet-based survey to surgeons resulted in a significantly lower response rate than a traditional mailed survey. Researchers should not assume that the widespread availability and potential ease of Internet-based surveys will translate into higher response rates. [Abstract/Link to Full Text]

Eysenbach G
Peer-review and publication of research protocols and proposals: a role for open access journals.
J Med Internet Res. 2004 Sep 30;6(3):e37.
Peer-review and publication of research protocols offer several advantages to all parties involved. Among these are the following opportunities for authors: external expert opinion on the methods, demonstration to funding agencies of prior expert review of the protocol, proof of priority of ideas and methods, and solicitation of potential collaborators. We think that review and publication of protocols is an important role for Open Access journals. Because of their electronic form, openness for readers, and author-pays business model, they are better suited than traditional journals to ensure the sustainability and quality of protocol reviews and publications. In this editorial, we describe the workflow for investigators in eHealth research, from protocol submission to a funding agency, to protocol review and (optionally) publication at JMIR, to registration of trials at the International eHealth Study Registry (IESR), and to publication of the report. One innovation at JMIR is that protocol peer reviewers will be paid a honorarium, which will be drawn partly from a new submission fee for protocol reviews. Separating the article processing fee into a submission and a publishing fee will allow authors to opt for "peer-review only" (without subsequent publication) at reduced costs, if they wish to await a funding decision or for other reasons decide not to make the protocol public. [Abstract/Link to Full Text]

Hart A, Henwood F, Wyatt S
The role of the Internet in patient-practitioner relationships: findings from a qualitative research study.
J Med Internet Res. 2004 Sep 30;6(3):e36.
BACKGROUND: Studies suggest that there has been an increase in the use of the Internet by patients in many Western societies. However, despite the many texts available on health and the Internet, not much is known about how much patients actually use the Internet to look up health information in their daily lives. We know little about what meaning this activity has for their experience of health and illness, and for their relationship with health-care practitioners. OBJECTIVE: To explore patients' and practitioners' use of the Internet and to consider whether use of the Internet is changing relationships between patients and health-care practitioners. METHOD: The study used qualitative interviews and observations of patient-practitioner interaction. Our purposive sample of 47 patients (32 women and 15 men) had all had contact with the health services for information/treatment in relation to hormone replacement therapy (HRT)/menopause and Viagra/erectile dysfunction. The setting for the research was in general practitioners' surgeries, specialist clinics and patients' homes in the United Kingdom. Participants reflected a wide range of socio-economic groups, but most were white and British born, which, given the ethnic make-up of the town in which we conducted the research, was not surprising. In addition to patients, we interviewed 10 health-care practitioners (4 consultant doctors, 3 GPs, 2 specialist nurses, and a psychologist) about their own health information seeking practices (HISPs) and those of their patients. RESULTS: Use of the Internet can increase patients' knowledge about their health conditions, although patients in our study were often too overwhelmed by the information available on the Internet to make an informed decision about their own care. Patients have a great deal of trust in their health-care practitioners. Health-care practitioners need to improve their own skills in Internet use. Hype around Internet use by patients appears to exceed the reality of Internet use. CONCLUSIONS: Our qualitative study suggests that use of the Internet is contributing to subtle changes in the relationship between health-care practitioners and their patients, rather than effecting the dramatic transformation some people envisage for it. [Abstract/Link to Full Text]

Eysenbach G
Tackling publication bias and selective reporting in health informatics research: register your eHealth trials in the International eHealth Studies Registry.
J Med Internet Res. 2004 Sep 30;6(3):e35.
Beginning in July 2005, several major medical journals, including the Journal of Medical Internet Research, will only consider trials for publication that have been registered in a trial registry before they started. This is to reduce publication bias and to prevent selective reporting of positive outcomes. As existing clinical trial registers seem to be unsuitable or suboptimal for eHealth studies, a free International eHealth Study Registry (IESR) has been set up, allowing registration of trials (including non-randomized studies) in the field of health informatics and assigning an International eHealth Study Number (IESN). The IESR should meet the requirements of journal editors for a-priori registration of a study. We hope IESR will become the preferred choice for registration of eHealth studies and, as an secondary benefit, will become an international repository of ongoing eHealth projects, thereby enhancing global collaboration and reducing duplication of effort. [Abstract/Link to Full Text]

Eysenbach G
Improving the quality of Web surveys: the Checklist for Reporting Results of Internet E-Surveys (CHERRIES).
J Med Internet Res. 2004 Sep 29;6(3):e34.
Analogous to checklists of recommendations such as the CONSORT statement (for randomized trials), or the QUORUM statement (for systematic reviews), which are designed to ensure the quality of reports in the medical literature, a checklist of recommendations for authors is being presented by the Journal of Medical Internet Research (JMIR) in an effort to ensure complete descriptions of Web-based surveys. Papers on Web-based surveys reported according to the CHERRIES statement will give readers a better understanding of the sample (self-)selection and its possible differences from a "representative" sample. It is hoped that author adherence to the checklist will increase the usefulness of such reports. [Abstract/Link to Full Text]

Demiris G
Disease management and the Internet.
J Med Internet Res. 2004 Sep 29;6(3):e33. [Abstract/Link to Full Text]

Wiecha J, Pollard T
The interdisciplinary eHealth team: chronic care for the future.
J Med Internet Res. 2004 Sep 3;6(3):e22.
An interdisciplinary clinical team is a consistent grouping of people from relevant clinical disciplines, ideally inclusive of the patient, whose interactions are guided by specific team functions and processes to achieve team-defined favorable patient outcomes. Teamwork supported by properly designed eHealth applications could help create more effective systems of care for chronic disease. Given its synchronous and asynchronous communication capacity and information-gathering and -sharing capabilities, the Internet is a logical platform for supporting interdisciplinary clinical teamwork. Research is needed to better understand how interdisciplinary eHealth team members can work together in everyday practice and to guide the development of effective and efficient eHealth software applications to support greater clinical teamwork. [Abstract/Link to Full Text]

Anhøj J, Nielsen L
Quantitative and qualitative usage data of an Internet-based asthma monitoring tool.
J Med Internet Res. 2004 Sep 3;6(3):e23.
BACKGROUND: In May 2000, AstraZeneca launched a Web service for asthma patients and health-care providers called LinkMedica, which includes an asthma diary for monitoring and self-management. In the diary, the patient enters his or her peak flow, number of doses of rescue medication, and if there have been any asthma symptoms during the previous 24 hours. The patient receives an immediate response from LinkMedica, telling him or her if the asthma is under control and what to do if not, eg, increase the dose of inhaled steroid. Health-care providers have access to the patient diary. OBJECTIVES: The primary objective of the study was to describe patients' and health-care providers' use of LinkMedica. Secondary objectives were to evaluate their perception of the system and how the users' interaction with the system is influenced by their everyday lives. METHODS: Site statistics regarding number of registered users and diary usage were analyzed. An online survey among users (85 respondents), a mailed questionnaire to health-care providers (131 respondents; response rate 26.8%), as well as in-depth interviews with 10 patients and 5 general practitioners, elicited further quantitative and qualitative data on users' perceptions. RESULTS: In February 2003, a total of 7653 users had registered. During 2002, the growth in registered users averaged 50 per month. In the same period, the number of unique diary users per month decreased from 307 to 138. Patients usually stopped using the diary after a short time; the doctors were reluctant to introduce the diary to patients because of time constraints. Several user subtypes were identified among patients and their relatives. CONCLUSION: The self-selected survey responses and in-depth interviews indicated that LinkMedica is generally considered a trustworthy and reliable site by both patients and doctors. However, there was a contrast between users' positive perception of LinkMedica and their unwillingness to use the site for more than short periods. The primary reason for this was that LinkMedica did not fit into their everyday lives because of technical and psychological aspects. A number of recommendations to improve LinkMedica are suggested. [Abstract/Link to Full Text]

Anhøj J, Jensen AH
Using the internet for life style changes in diet and physical activity: a feasibility study.
J Med Internet Res. 2004 Sep 8;6(3):e28.
BACKGROUND: LinkMedica-Heart is a novel Internet based program intended to support people who seek to improve their life style by means of changes in diet and physical activity. The program is currently under evaluation in a clinical study and the present study is a feasibility test of the LinkMedica-Heart Internet based program. OBJECTIVE: The aim of this study was to evaluate LinkMedica-Heart, an Internet based program we designed for support and maintenance of patient-led life style changes. METHODS: The feasibility study of LinkMedica-Heart presented here is a qualitative study. Nine general practitioners were invited to participate. Each practitioner was asked to introduce LinkMedica-Heart to not less than two patients, with a maximum of five patients per practitioner. Patients and general practitioners were both asked to participate in testing the program for a period of 6 months. At the end of 6 months, evaluation meetings were held with the general practitioners, and separate interviews took place with some of the participating patients who were selected by the GPs. RESULTS: Five general practitioners and 25 patients participated in the study. The general practitioners and the patients were enthusiastic about the prospect of an Internet based life style change program. However, the program was not able to sustain patient loyalty over an extended period. The doctors found that the program was much too complicated to navigate and that the results from the program could not be trusted. The patients in contrast had fewer complaints about the program design, but found that the advice given by the program was too elaborate and detailed and, in general, did not add to the patient's knowledge on life style change. CONCLUSION: Our study confirms that there is a need for, and a receptive attitude toward a Web-based program that supports people who want to improve their life style and health. LinkMedica-Heart in its present form does not satisfy these needs. We suggest a number of design changes and improvements to the program. [Abstract/Link to Full Text]

Flicker S, Goldberg E, Read S, Veinot T, McClelland A, Saulnier P, Skinner H
HIV-positive youth's perspectives on the Internet and e-health.
J Med Internet Res. 2004 Sep 29;6(3):e32.
BACKGROUND: Globally, half of all new HIV infections occur among young people. Despite this incidence, there is a profound lack of resources for HIV-positive youth. OBJECTIVE: To investigate Internet access, use and acceptability as means for health promotion and health service delivery among HIV-positive youth. METHODS: A community-based participatory approach was used to conduct a mixed methods research study. Thirty-five qualitative in-depth semi-structured interviews were conducted with youth (ages 12-24) living with HIV in Ontario. Also, brief structured demographic surveys were administered at the time of the interview. A stakeholder group of youth living with HIV, professionals and researchers collaboratively analyzed the data for emerging themes. RESULTS: Five main themes were identified with respect to the youth's use of and interest in the Internet as a health promotion strategy. These include: (1) high rates of Internet use and access; (2) issues around public and private terminals; (3) their use of the Internet primarily for communication and entertainment; (4) the rarity of health information seeking behavior in this group; and (5) wanting "one-stop shopping" from an e-health site. HIV-positive youth were enthusiastic about the possibility of content that was developed specifically to target them and their needs. Also, they were keen about the possibilities for increased social support that youth-specific online chat rooms and message boards might provide. CONCLUSION: Given high rates of use, access and interest, the Internet provides an important way to reach young people living with HIV using health services and health promotion programs. The onus is on e-Health developers to understand the particular needs of HIV-positive youth and create relevant content. [Abstract/Link to Full Text]

Schonlau M
Will web surveys ever become part of mainstream research?
J Med Internet Res. 2004 Sep 23;6(3):e31. [Abstract/Link to Full Text]

Ritter P, Lorig K, Laurent D, Matthews K
Internet versus mailed questionnaires: a randomized comparison.
J Med Internet Res. 2004 Sep 15;6(3):e29.
BACKGROUND: The use of Internet-based questionnaires for collection of data to evaluate patient education and other interventions has increased in recent years. Many self-report instruments have been validated using paper-and-pencil versions, but we cannot assume that the psychometric properties of an Internet-based version will be identical. OBJECTIVES: To look at similarities and differences between the Internet versions and the paper-and-pencil versions of 16 existing self-report instruments useful in evaluation of patient interventions. METHODS: Participants were recruited via the Internet and volunteered to participate (N=397), after which they were randomly assigned to fill out questionnaires online or via mailed paper-and-pencil versions. The self-report instruments measured were overall health, health distress, practice mental stress management, Health Assessment Questionnaire (HAQ) disability, illness intrusiveness, activity limitations, visual numeric for pain, visual numeric for shortness of breath, visual numeric for fatigue, self-efficacy for managing disease, aerobic exercise, stretching and strengthening exercise, visits to MD, hospitalizations, hospital days, and emergency room visits. Means, ranges, and confidence intervals are given for each instrument within each type of questionnaire. The results from the two questionnaires were compared using both parametric and non-parametric tests. Reliability tests were given for multi-item instruments. A separate sample (N=30) filled out identical questionnaires over the Internet within a few days and correlations were used to assess test-retest reliability. RESULTS: Out of 16 instruments, none showed significant differences when the appropriate tests were used. Construct reliability was similar within each type of questionnaire, and Internet test-retest reliability was high. Internet questionnaires required less follow-up to achieve a slightly (non-significant) higher completion rate compared to mailed questionnaires. CONCLUSIONS: Among a convenience sample recruited via the Internet, results from those randomly assigned to Internet participation were at least as good as, if not better than, among those assigned mailed questionnaires, with less recruitment effort required. The instruments administered via the Internet appear to be reliable, and to be answered similarly to the way they are answered when they are administered via traditional mailed paper questionnaires. [Abstract/Link to Full Text]

Plovnick RM, Zeng QT
Reformulation of consumer health queries with professional terminology: a pilot study.
J Med Internet Res. 2004 Sep 3;6(3):e27.
BACKGROUND: The Internet is becoming an increasingly important resource for health-information seekers. However, consumers often do not use effective search strategies. Query reformulation is one potential intervention to improve the effectiveness of consumer searches. OBJECTIVE: We endeavored to answer the research question: "Does reformulating original consumer queries with preferred terminology from the Unified Medical Language System (UMLS) Metathesaurus lead to better search returns?" METHODS: Consumer-generated queries with known goals (n=16) that could be mapped to UMLS Metathesaurus terminology were used as test samples. Reformulated queries were generated by replacing user terms with Metathesaurus-preferred synonyms (n=18). Searches (n=36) were performed using both a consumer information site and a general search engine. Top 30 precision was used as a performance indicator to compare the performance of the original and reformulated queries. RESULTS: Forty-two percent of the searches utilizing reformulated queries yielded better search returns than their associated original queries, 19% yielded worse results, and the results for the remaining 39% did not change. We identified ambiguous lay terms, expansion of acronyms, and arcane professional terms as causes for changes in performance. CONCLUSIONS: We noted a trend towards increased precision when providing substitutions for lay terms, abbreviations, and acronyms. We have found qualitative evidence that reformulating queries with professional terminology may be a promising strategy to improve consumer health-information searches, although we caution that automated reformulation could in fact worsen search performance when the terminology is ill-fitted or arcane. [Abstract/Link to Full Text]

Birru M, Steinman RA
Online health information and low-literacy African Americans.
J Med Internet Res. 2004 Sep 3;6(3):e26.
African Americans with low incomes and low literacy levels disproportionately suffer poor health outcomes from many preventable diseases. Low functional literacy and low health literacy impede millions of Americans from successfully accessing health information. These problems are compounded for African Americans by cultural insensitivity in health materials. The Internet could become a useful tool for providing accessible health information to low-literacy and low-income African Americans. Optimal health Web sites should include text written at low reading levels and appropriate cultural references. More research is needed to determine how African Americans with low literacy skills access, evaluate, prioritize, and value health information on the Internet. [Abstract/Link to Full Text]

Birru MS, Monaco VM, Charles L, Drew H, Njie V, Bierria T, Detlefsen E, Steinman RA
Internet usage by low-literacy adults seeking health information: an observational analysis.
J Med Internet Res. 2004 Sep 3;6(3):e25.
BACKGROUND: Adults with low literacy may encounter informational obstacles on the Internet when searching for health information, in part because most health Web sites require at least a high-school reading proficiency for optimal access. OBJECTIVE: The purpose of this study was to 1) determine how low-literacy adults independently access and evaluate health information on the Internet, 2) identify challenges and areas of proficiency in the Internet-searching skills of low-literacy adults. METHODS: Subjects (n=8) were enrolled in a reading assistance program at Bidwell Training Center in Pittsburgh, PA, and read at a 3rd to 8th grade level. Subjects conducted self-directed Internet searches for designated health topics while utilizing a think-aloud protocol. Subjects' keystrokes and comments were recorded using Camtasia Studio screen-capture software. The search terms used to find health information, the amount of time spent on each Web site, the number of Web sites accessed, the reading level of Web sites accessed, and the responses of subjects to questionnaires were assessed. RESULTS: Subjects collectively answered 8 out of 24 questions correctly. Seven out of 8 subjects selected "sponsored sites"-paid Web advertisements-over search engine-generated links when answering health questions. On average, subjects accessed health Web sites written at or above a 10th grade reading level. Standard methodologies used for measuring health literacy and for promoting subjects to verbalize responses to Web-site form and content had limited utility in this population. CONCLUSION: This study demonstrates that Web health information requires a reading level that prohibits optimal access by some low-literacy adults. These results highlight the low-literacy adult population as a potential audience for Web health information, and indicate some areas of difficulty that these individuals face when using the Internet and health Web sites to find information on specific health topics. [Abstract/Link to Full Text]

Walther JB, Wang Z, Loh T
The effect of top-level domains and advertisements on health web-site credibility.
J Med Internet Res. 2004 Sep 3;6(3):e24.
BACKGROUND: Concerns over health information on the Internet have generated efforts to enhance credibility markers; yet how users actually assess the credibility of online health information is largely unknown. OBJECTIVE: This study set out to (1) establish a parsimonious and valid questionnaire instrument to measure credibility of Internet health information by drawing on various previous measures of source, news, and other credibility scales; and (2) to identify the effects of Web-site domains and advertising on credibility perceptions. METHODS: Respondents (N = 156) examined one of 12 Web-site mock-ups and completed credibility scales in a 3 x 2 x 2 between-subjects experimental design. Factor analysis and validity checks were used for item reduction, and analysis of variance was employed for hypothesis testing of Web-site features' effects. RESULTS: In an attempt to construct a credibility instrument, three dimensions of credibility (safety, trustworthiness, and dynamism) were retained, reflecting traditional credibility sub-themes, but composed of items from disparate sources. When testing the effect of the presence or absence of advertising on a Web site on credibility, we found that this depends on the site's domain, with a trend for advertisements having deleterious effects on the credibility of sites with .org domain, but positive effects on sites with .com or .edu domains. CONCLUSIONS: Health-information Web-site providers should select domains purposefully when they can, especially if they must accept on-site advertising. Credibility perceptions may not be invariant or stable, but rather are sensitive to topic and context. Future research may employ these findings in order to compare other forms of health-information delivery to optimal Web-site features. [Abstract/Link to Full Text]

Walji M, Sagaram S, Sagaram D, Meric-Bernstam F, Johnson C, Mirza NQ, Bernstam EV
Efficacy of quality criteria to identify potentially harmful information: a cross-sectional survey of complementary and alternative medicine web sites.
J Med Internet Res. 2004 Jun 29;6(2):e21.
BACKGROUND: Many users search the Internet for answers to health questions. Complementary and alternative medicine (CAM) is a particularly common search topic. Because many CAM therapies do not require a clinician's prescription, false or misleading CAM information may be more dangerous than information about traditional therapies. Many quality criteria have been suggested to filter out potentially harmful online health information. However, assessing the accuracy of CAM information is uniquely challenging since CAM is generally not supported by conventional literature. OBJECTIVE: The purpose of this study is to determine whether domain-independent technical quality criteria can identify potentially harmful online CAM content. METHODS: We analyzed 150 Web sites retrieved from a search for the three most popular herbs: ginseng, ginkgo and St. John's wort and their purported uses on the ten most commonly used search engines. The presence of technical quality criteria as well as potentially harmful statements (commissions) and vital information that should have been mentioned (omissions) was recorded. RESULTS: Thirty-eight sites (25%) contained statements that could lead to direct physical harm if acted upon. One hundred forty five sites (97%) had omitted information. We found no relationship between technical quality criteria and potentially harmful information. CONCLUSIONS: Current technical quality criteria do not identify potentially harmful CAM information online. Consumers should be warned to use other means of validation or to trust only known sites. Quality criteria that consider the uniqueness of CAM must be developed and validated. [Abstract/Link to Full Text]

Kind T, Wheeler KL, Robinson B, Cabana MD
Do the leading children's hospitals have quality web sites? A description of children's hospital web sites.
J Med Internet Res. 2004 Jun 25;6(2):e20.
BACKGROUND: Although leading children's hospitals are recognized as preeminent in the provision of health care to children, the quality of their Web sites has not been described. OBJECTIVE: To describe technical characteristics of the Web sites of leading children's hospitals. METHODS: This is a cross-sectional descriptive infodemiology study. Two reviewers independently reviewed and analyzed the Web sites of 26 nationally prominent children's hospitals in June 2003, using objective criteria based on accessibility (based on age and language), attribution, completeness, credibility, currency, disclosure, readability, and other technical elements. RESULTS: One-third of Web sites included content for children and adolescents. Twenty-four (92%) of the Web sites had health and disease-specific information. One-third contained only English, while two-thirds included other languages. All 26 Web sites included a disclaimer, although none had a requirement to read the disclaimer before accessing health and disease specific information. Twenty-four (92%) had search options. Although most (85%) listed a copyright date, only 10% listed the date last updated. CONCLUSIONS: This is the first study to examine the Web sites of leading children's hospitals. Although the Web sites were designed for children's hospitals, only a few sites included content for children and adolescents. Primary care physicians who refer patients to these sites should be aware that many have limited content for children, and should assess them for other limitations, such as inconsistent documentation of disclaimers or failure to show the date of the last Web site update. These Web sites are a potentially useful source of patient information. However, as the public increasingly looks to the Internet for health information, children's hospitals need to keep up with increasingly high standards and demands of health-care consumers. [Abstract/Link to Full Text]

Zeng X, Parmanto B
Web content accessibility of consumer health information web sites for people with disabilities: a cross sectional evaluation.
J Med Internet Res. 2004 Jun 21;6(2):e19.
BACKGROUND: The World Wide Web (WWW) has become an increasingly essential resource for health information consumers. The ability to obtain accurate medical information online quickly, conveniently and privately provides health consumers with the opportunity to make informed decisions and participate actively in their personal care. Little is known, however, about whether the content of this online health information is equally accessible to people with disabilities who must rely on special devices or technologies to process online information due to their visual, hearing, mobility, or cognitive limitations. OBJECTIVE: To construct a framework for an automated Web accessibility evaluation; to evaluate the state of accessibility of consumer health information Web sites; and to investigate the possible relationships between accessibility and other features of the Web sites, including function, popularity and importance. METHODS: We carried out a cross-sectional study of the state of accessibility of health information Web sites to people with disabilities. We selected 108 consumer health information Web sites from the directory service of a Web search engine. A measurement framework was constructed to automatically measure the level of Web Accessibility Barriers (WAB) of Web sites following Web accessibility specifications. We investigated whether there was a difference between WAB scores across various functional categories of the Web sites, and also evaluated the correlation between the WAB and Alexa traffic rank and Google Page Rank of the Web sites. RESULTS: We found that none of the Web sites we looked at are completely accessible to people with disabilities, i.e., there were no sites that had no violation of Web accessibility rules. However, governmental and educational health information Web sites do exhibit better Web accessibility than the other categories of Web sites (P < 0.001). We also found that the correlation between the WAB score and the popularity of a Web site is statistically significant (r = 0.28, P < 0.05), although there is no correlation between the WAB score and the importance of the Web sites (r = 0.15, P = 0.111). CONCLUSIONS: Evaluation of health information Web sites shows that no Web site scrupulously abides by Web accessibility specifications, even for entities mandated under relevant laws and regulations. Government and education Web sites show better performance than Web sites among other categories. Accessibility of a Web site may have a positive impact on its popularity in general. However, the Web accessibility of a Web site may not have a significant relationship with its importance on the Web. [Abstract/Link to Full Text]

Greenberg L, D'Andrea G, Lorence D
Setting the public agenda for online health search: a white paper and action agenda.
J Med Internet Res. 2004 Jun 8;6(2):e18.
BACKGROUND: Searches for health information are among the most common reasons that consumers use the Internet. Both consumers and quality experts have raised concerns about the quality of information on the Web and the ability of consumers to find accurate information that meets their needs. OBJECTIVE: To produce a national stakeholder-driven agenda for research, technical improvements, and education that will improve the results of consumer searches for health information on the Internet. METHODS: URAC, a national accreditation organization, and Consumer WebWatch (CWW), a project of Consumers Union (a consumer advocacy organization), conducted a review of factors influencing the results of online health searches. The organizations convened two stakeholder groups of consumers, quality experts, search engine experts, researchers, health-care providers, informatics specialists, and others. Meeting participants reviewed existing information and developed recommendations for improving the results of online consumer searches for health information. Participants were not asked to vote on or endorse the recommendations. Our working definition of a quality Web site was one that contained accurate, reliable, and complete information. RESULTS: The Internet has greatly improved access to health information for consumers. There is great variation in how consumers seek information via the Internet, and in how successful they are in searching for health information. Further, there is variation among Web sites, both in quality and accessibility. Many Web site features affect the capability of search engines to find and index them. CONCLUSIONS: Research is needed to define quality elements of Web sites that could be retrieved by search engines and understand how to meet the needs of different types of searchers. Technological research should seek to develop more sophisticated approaches for tagging information, and to develop searches that "learn" from consumer behavior. Finally, education initiatives are needed to help consumers search more effectively and to help them critically evaluate the information they find. [Abstract/Link to Full Text]

Eminovic N, Wyatt JC, Tarpey AM, Murray G, Ingrams GJ
First evaluation of the NHS direct online clinical enquiry service: a nurse-led web chat triage service for the public.
J Med Internet Res. 2004 Jun 2;6(2):e17.
BACKGROUND: NHS Direct is a telephone triage service used by the UK public to contact a nurse for any kind of health problem. NHS Direct Online (NHSDO) extends NHS Direct, allowing the telephone to be replaced by the Internet, and introducing new opportunities for informing patients about their health. One NHSDO service under development is the Clinical Enquiry Service (CES), which uses Web chat as the communication medium. OBJECTIVE: To identify the opportunities and possible risks of such a service by exploring its safety, feasibility, and patient perceptions about using Web chat to contact a nurse. METHODS: During a six-day pilot performed in an inner-city general practice in Coventry, non-urgent patients attending their GP were asked to test the service. After filling out three Web forms, patients used a simple Web chat application to communicate with trained NHS Direct triage nurses, who responded with appropriate triage advice. All patients were seen by their GP immediately after using the Web chat service. Safety was explored by comparing the nurse triage end point with the GP's recommended end point. In order to check the feasibility of the service, we measured the duration of the chat session. Patient perceptions were measured before and after using the service through a modified Telemedicine Perception Questionnaire (TMPQ) instrument. All patients were observed by a researcher who captured any comments and, if necessary, to assisted with the process. RESULTS: A total of 25 patients (mean age 48 years; 57% female) agreed to participate in the study. An exact match between the nurse and the GP end point was found in 45% (10/22) of cases. In two cases, the CES nurse proposed a less urgent end point than the GP. The median duration of Web chat sessions was 30 minutes, twice the median for NHS Direct telephone calls for 360 patients with similar presenting problems. There was a significant improvement in patients' perception of CES after using the service (mean pre-test TMPQ score 44/60, post-test 49/60; p=0.008 (2-tailed)). Patients volunteered several potential advantages of CES, such as the ability to re-read the answers from the nurse. Patients consider CES a useful addition to regular care, but not a replacement for it. CONCLUSIONS: Based on this pilot, we can conclude that CES was sufficiently safe to continue piloting, but in order to make further judgments about safety, more tests with urgent cases should be performed. The Web chat sessions as conducted were too long and therefore too expensive to be sustainable in the NHS. However, the positive reaction from patients and the potential of CES for specific patient groups (the deaf, shy, or socially isolated) encourage us to continue with piloting such innovative communication methods with the public. [Abstract/Link to Full Text]

Enzenhofer M, Bludau HB, Komm N, Wild B, Mueller K, Herzog W, Hochlehnert A
Improvement of the educational process by computer-based visualization of procedures: randomized controlled trial.
J Med Internet Res. 2004 Jun 2;6(2):e16.
BACKGROUND: Before any invasive procedure, physicians have a legal obligation to inform patients. Traditionally, this involves a discussion with a physician, supplemented by written leaflet information directed at the specific procedure. OBJECTIVE: Comparison of the use and effectiveness of computer-based visualization opposed to standardized conversation for providing patients with information of forthcoming procedures (coronary catheters or endoscopy procedures). METHODS: Prospective, randomized trial with 56 participants allocated in two different groups: Visualization Group (standardized information supported by a tool for displaying two-dimensional pictures to explain medical facts as well as informative leaflet) or Control Group (standardized information and informative leaflet only). Detailed information was given about the indication, the probable complications and the details of the forthcoming procedures (coronary catheters or endoscopy procedures). All participants had to reach a Karnofsky Score of 70 points and be able to understand German or English. Main outcome measures were patient's satisfaction with physician-patient conversation, patient's acquired knowledge and duration of the intervention as described above. RESULTS: Patients of the Visualization Group were more satisfied with the conversation and had higher knowledge scores after the conversation. A Mann-Whitney-U-Test between the two groups showed that these differences in satisfaction (P<0.001) and knowledge (P= or <0.006) were statistically significant. Length of time needed for the conversation was slightly higher in the Visualization Group, but this difference was not statistically significant (25 versus 23 min; P= 0.441). No differences could be found due to differing age or educational level in the results of the Visualization and the Control Group. CONCLUSIONS: Using computerized visualization increased the satisfaction and knowledge of the patients. The presentation of the visualized information in the Visualization Group did not demand significantly more time than the standard conversation in the Control Group. [Abstract/Link to Full Text]

Dutta-Bergman MJ
Health attitudes, health cognitions, and health behaviors among Internet health information seekers: population-based survey.
J Med Internet Res. 2004 May 28;6(2):e15.
BACKGROUND: Using a functional theory of media use, this paper examines the process of health-information seeking in different domains of Internet use. OBJECTIVE: Based on an analysis of the 1999 HealthStyles data, this study was designed to demonstrate that people who gather information on the Internet are more health-oriented than non-users of Internet health information. METHODS: The Porter Novelli HealthStyles database, collected annually since 1995, is based on the results of nationally representative postal mail surveys. In 1999, 2636 respondents provided usable data for the HealthStyles database. Independent sample t-tests and logistic regression analyses were conducted. RESULTS: The results showed that individuals who searched for health information on the Internet were indeed more likely to be health-oriented than those who did not. Consumers who sought out medical information on the Internet reported higher levels of health-information orientation and healthy activities, as well as stronger health beliefs than those who did not search for medical news on the Internet. It was observed that those who reported searching for information about drugs and medications on the Internet held stronger health beliefs than the non-searchers. Comparison of individuals who reported seeking out information about specific diseases on the Internet with individuals who did not showed those who sought out disease-specific information on the Internet to be more health-oriented. Finally, consumers who sought out healthy lifestyle information on the Internet were more health conscious and more health-information oriented than those who did not. They were also more likely to hold stronger health-oriented beliefs and to engage in healthy activities. CONCLUSIONS: The results support the functional theory of Internet use. Internet searchers who used the Internet for a wide range of health purposes were typically more health oriented than non-searchers. [Abstract/Link to Full Text]

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Recent Articles in BMC Bioinformatics

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Sjogren A, Kristiansson E, Rudemo M, Nerman O
Weighted analysis of general microarray experiments.
BMC Bioinformatics. 2007 Oct 15;8(1):387.
ABSTRACT: BACKGROUND: In DNA microarray experiments, measurements from different biological samples are often assumed to be independent and to have identical variance. For many datasets these assumptions have been shown to be invalid and typically lead to too optimistic p-values. A method called WAME has been proposed where a variance is estimated for each sample and a covariance is estimated for each pair of samples. The current version of WAME is, however, limited to experiments with paired design, e.g. two-channel microarrays. RESULTS: The WAME procedure is extended to general microarray experiments, making it capable of handling both one- and two-channel datasets. Two public one-channel datasets are analysed and WAME detects both unequal variances and correlations. WAME is compared to other common methods: fold-change ranking, ordinary linear model with t-tests, LIMMA and weighted LIMMA. The p-value distributions are shown to differ greatly between the examined methods. In a resampling-based simulation study, the p-values generated by WAME are found to be substantially more correct than the alternatives when a relatively small proportion of the genes is regulated. WAME is also shown to have higher power than the other methods. WAME is available as an R-package. CONCLUSIONS: The WAME procedure is generalized and the limitation to paired-design microarray datasets is removed. The examined other methods produce invalid p-values in many cases, while WAME is shown to produce essentially valid p-values when a relatively small proportion of genes is regulated. WAME is also shown to have higher power than the examined alternative methods. [Abstract/Link to Full Text]

Froehlich H, Fellmann M, Sueltmann H, Poustka A, Beissbarth T
Large scale statistical inference of signaling pathways from RNAi and microarray data.
BMC Bioinformatics. 2007 Oct 15;8(1):386.
ABSTRACT: BACKGROUND: The advent of RNA interference techniques enables the selective silencing of biologically interesting genes in an efficient way. In combination with DNA microarray technology this enables researchers to gain insights into genetic signaling pathways by observing downstream effects of individual knock-downs on gene expression. These secondary effects can be used to computationally reverse engineer features of the upstream signaling pathway. RESULTS: In this paper we address this challenging problem by extending previous work by Markowetz et al., who proposed a statistical framework to score networks hypotheses in a Bayesian manner. Our extensions go in three directions: First, we introduce a way to omit the data discretization step needed in the original framework via a calculation based on p-values instead. Second, we show how prior assumptions on the network structure can be incorporated into the scoring scheme using regularization techniques. Third and most importantly, we propose methods to scale up the original approach, which is limited to around 5 genes, to large scale networks. CONCLUSIONS: Comparisons of these methods on artificial data are conducted. Our proposed module network is employed to infer the signaling network between 13 genes in the ER-alpha pathway in human MCF-7 breast cancer cells. Using a bootstrapping approach this reconstruction can be found with good statistical stability. The code for the module network inference method is available in the latest version of the R-package - nem, which can be obtained from the Bioconductor homepage. [Abstract/Link to Full Text]

Redhead E, Bailey TL
Discriminative motif discovery in DNA and protein sequences using the DEME Algorithm.
BMC Bioinformatics. 2007 Oct 15;8(1):385.
ABSTRACT: BACKGROUND: Motif discovery aims to detect short, highly conserved patterns in a collection of unaligned DNA or protein sequences. Discriminative motif finding algorithms aim to increase the sensitivity and selectivity of motif discovery by utilizing a second set of sequences, and searching only for patterns that can differentiate the two sets of sequences. Potential applications of discriminative motif discovery include discovering transcription factor binding site motifs in ChIP-chip data and finding protein motifs involved in thermal stability using sets of orthologous proteins from thermophilic and mesophilic organisms. RESULTS: We describe DEME, a discriminative motif discovery algorithm for use with protein and DNA sequences. Input to DEME is two sets of sequences--a "positive" set and a "negative" set. DEME represents motifs using a probabilistic model, and uses a novel combination of global and local search to find the motif that optimally discriminates between the two sets of sequences. DEME is unique among discriminative motif finders in that it uses an informative Bayesian prior on protein motif columns, allowing it to incorporate prior knowledge of residue characteristics. We also introduce four, synthetic problems that are designed for evaluating discriminative motif finders in various biologically motivated contexts. We test DEME using these problems and on two biological problems: finding yeast transcription factor binding motifs in ChIP-chip data, and finding motifs that discriminate between groups of thermophilic and mesophilic orthologous proteins. CONCLUSIONS: Using artificial data, we show that DEME is more effective than a non-discriminative approach when there are "decoy" motifs or when a variant of the motif is present in the "negative" sequences. With real data, we show that DEME is as good, but not better than non-discriminative algorithms at discovering yeast transcription factor binding motifs. We also show that DEME can find highly informative thermal-stability protein motifs. Source code in C for the stand-alone program DEME is free for academic use and is available at: http://bioinformatics.org.au/deme/ [Abstract/Link to Full Text]

Kwon YK, Choi SS, Cho KH
Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling.
BMC Bioinformatics. 2007;8384.
BACKGROUND: A number of studies on biological networks have been carried out to unravel the topological characteristics that can explain the functional importance of network nodes. For instance, connectivity, clustering coefficient, and shortest path length were previously proposed for this purpose. However, there is still a pressing need to investigate another topological measure that can better describe the functional importance of network nodes. In this respect, we considered a feedback loop which is ubiquitously found in various biological networks. RESULTS: We discovered that the number of feedback loops (NuFBL) is a crucial measure for evaluating the importance of a network node and verified this through a signal transduction network in the hippocampal CA1 neuron of mice as well as through generalized biological network models represented by Boolean networks. In particular, we observed that the proteins with a larger NuFBL are more likely to be essential and to evolve slowly in the hippocampal CA1 neuronal signal transduction network. Then, from extensive simulations based on the Boolean network models, we proved that a network node with the larger NuFBL is likely to be more important as the mutations of the initial state or the update rule of such a node made the network converge to a different attractor. These results led us to infer that such a strong positive correlation between the NuFBL and the importance of a network node might be an intrinsic principle of biological networks in view of network dynamics. CONCLUSION: The presented analysis on topological characteristics of biological networks showed that the number of feedback loops is positively correlated with the functional importance of network nodes. This result also suggests the existence of unknown feedback loops around functionally important nodes in biological networks. [Abstract/Link to Full Text]

Vencio RZ, Shmulevich I
ProbCD: enrichment analysis accounting for categorization uncertainty.
BMC Bioinformatics. 2007 Oct 12;8(1):383.
ABSTRACT: BACKGROUND: As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. RESULTS: We developed an open-source R-based software to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table for the enrichment problem is built using the expectation of a Bernoulli Scheme stochastic process given the categorization probabilities. An on-line interface was created to allow usage by non-programmers and is available at: http://xerad.systemsbiology.net/ProbCD/. CONCLUSIONS: We present an analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques and (ii) probabilistic gene annotation. [Abstract/Link to Full Text]

Newman AM, Cooper JB
XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences.
BMC Bioinformatics. 2007 Oct 11;8(1):382.
ABSTRACT: BACKGROUND: Biological sequence repeats arranged in tandem patterns are widespread in DNA and proteins. While many software tools have been designed to detect DNA tandem repeats (TRs), useful algorithms for identifying protein TRs with varied levels of degeneracy are still needed. RESULTS: To address limitations of current repeat identification methods, and to provide an efficient and flexible algorithm for the detection and analysis of TRs in protein sequences, we designed and implemented a new computational method called XSTREAM. Running time tests confirm the practicality of XSTREAM for analyses of multi-genome datasets. Each of the key capabilities of XSTREAM (e.g., merging, nesting, long-period detection, and TR architecture modeling) are demonstrated using anecdotal examples, and the utility of XSTREAM for identifying TR proteins was validated using data from a recently published paper. CONCLUSIONS: We show that XSTREAM is a practical and valuable tool for TR detection in protein and nucleotide sequences at the multi-genome scale, and an effective tool for modeling TR domains with diverse architectures and varied levels of degeneracy. Because of these useful features, XSTREAM has significant potential for the discovery of naturally-evolved modular proteins with applications for engineering novel biostructural and biomimetic materials, and identifying new vaccine and diagnostic targets. [Abstract/Link to Full Text]

Caffrey DR, Dana PH, Mathur V, Ocano M, Hong EJ, Wang YE, Somaroo S, Caffrey BE, Potluri S, Huang ES
PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments.
BMC Bioinformatics. 2007;8381.
BACKGROUND: By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. RESULTS: Here we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple annotations is a key component of this release as it provides a framework for most of the new functionalities. The sequence annotations are accessible from the alignment and tree, where they are typically used to label sequences or hyperlink them to related databases. Sequence annotations can be created manually or extracted automatically from UniProt entries. Once a multiple sequence alignment is populated with sequence annotations, sequences can be easily selected and sorted through a sophisticated search dialog. The selected sequences can be further analyzed using statistical methods that explicitly model relationships between the sequence annotations and residue properties. Residue annotations are accessible from the alignment viewer and are typically used to designate binding sites or properties for a particular residue.Residue annotations are also searchable, and allow one to quickly select alignment columns for further sequence analysis, e.g. computing percent identities. Other features include: novel algorithms to compute sequence conservation, mapping conservation scores to a 3D structure in Jmol, displaying secondary structure elements, and sorting sequences by residue composition. CONCLUSION: PFAAT provides a framework whereby end-users can specify knowledge for a protein family in the form of annotation. The annotations can be combined with sophisticated analysis to test hypothesis that relate to sequence, structure and function. [Abstract/Link to Full Text]

Carugo O
Detailed estimation of bioinformatics prediction reliability through the Fragmented Prediction Performance Plots.
BMC Bioinformatics. 2007 Oct 11;8(1):380.
ABSTRACT: BACKGROUND: An important and yet rather neglected question related to bioinformatics predictions is the estimation of the amount of data that is needed to allow reliable predictions. Bioinformatics predictions are usually validated through a series of figures of merit, like for example sensitivity and precision, and little attention is paid to the fact that their performance may depend on the amount of data used to make the predictions themselves. RESULTS: Here I describe a tool, named Fragmented Prediction Performance Plot (FPPP), which monitors the relationship between the prediction reliability and the amount of information underling the prediction themselves. Three examples of FPPPs are presented to illustrate their principal features. In one example, the reliability becomes independent, over a certain threshold, of the amount of data used to predict protein features and the intrinsic reliability of the predictor can be estimated. In the other two cases, on the contrary, the reliability strongly depends on the amount of data used to make the predictions and, thus, the intrinsic reliability of the two predictors cannot be determined. Only in the first example it is thus possible to fully quantify the prediction performance. CONCLUSIONS: It is thus highly advisable to use FPPPs to determine the performance of any new bioinformatics prediction protocol, in order to fully quantify its prediction power and to allow comparisons between two or more predictors based on different types of data. [Abstract/Link to Full Text]

Zhu D, Fox GE, Chakravarty S
RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguish among these viruses.
BMC Bioinformatics. 2007 Oct 10;8(1):379.
ABSTRACT: BACKGROUND: Most single stranded RNA (ssRNA) viruses mutate rapidly to generate large number of strains having highly divergent capsid sequences. Accurate strain recognition in uncharacterized target capsid sequences is essential for epidemiology, diagnostics, and vaccine development. Strain recognition based on similarity scores between target sequences and sequences of homology matched reference strains is often time consuming and ambiguous. This is especially true if only partial target sequences are available or if different ssRNA virus families are jointly analyzed. In such cases, knowledge of residues that uniquely distinguish among known reference strains is critical for rapid and unambiguous strain identification. Conventional sequence comparisons are unable to identify such capsid residues due to high sequence divergence among the ssRNA virus reference strains. Consequently, automated general methods to reliably identify strains using strain distinguishing residues are not currently available. RESULTS: We present here RECOVIR ("recognize viruses"), a software tool to automatically detect strains of caliciviruses and picornaviruses by comparing their capsid residues with built-in databases of residues that uniquely distinguish among known reference strains of these viruses. The databases were created by constructing partitioned phylogenetic trees of complete capsid sequences of these viruses. Strains were correctly identified for more than 300 complete and partial target sequences by comparing the database residues with the aligned residues of these sequences. It required about 5 seconds of real time to process each sequence. A Java-based user interface coupled with Perl-coded computational modules ensures high portability of the software. RECOVIR currently runs on Windows XP and Linux platforms. The software generalizes a manual method briefly outlined earlier for human caliciviruses. CONCLUSIONS: This study shows implementation of an automated method to identify virus strains using databases of capsid residues. The method is implemented to detect strains of caliciviruses and picornaviruses, two of the most highly divergent ssRNA virus families, and therefore, especially difficult to identify using uniform criteria. It is feasible to incorporate the approach into classification schemes of caliciviruses and picornaviruses and to extend the approach to recognize and classify other ssRNA virus families. [Abstract/Link to Full Text]

Ward WO, Swartz CD, Porwollik S, Warren SH, Hanley NM, McClelland M, Demarini DM
Toxicogenomic analysis incorporating operon-transcriptional coupling and toxicant concentration-expression response: anaysis of MX-treated Salmonella.
BMC Bioinformatics. 2007 Oct 9;8(1):378.
ABSTRACT: BACKGROUND: Deficiencies in microarray technology cause unwanted variation in the hybridization signal, obscuring the true measurements of intracellular transcript levels. Here we describe a general method that can improve microarray analysis of toxicant-exposed cells that uses the intrinsic power of transcriptional coupling and toxicant concentration-expression response data. To illustrate this approach, we characterized changes in global gene expression induced in Salmonella typhimurium TA100 by 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX), the primary mutagen in chlorinated drinking water. We used the co-expression of genes within an operon and the monotonic increases or decreases in gene expression relative to increasing toxicant concentration to augment our identification of differentially expressed genes beyond Bayesian-t analysis. RESULTS: Operon analysis increased the number of altered genes by 95% from the list identified by a Bayesian t-test of control to the highest concentration of MX. Monotonic analysis added 46% more genes. A functional analysis of the resulting 448 differentially expressed genes yielded functional changes beyond what would be expected from only the mutagenic properties of MX. In addition to gene-expression changes in DNA-damage response, MX induced changes in expression of genes involved in membrane transport and porphyrin metabolism, among other biological processes. The disruption of porphyrin metabolism might be attributable to the structural similarity of MX, which is a chlorinated furanone, to ligands indigenous to the porphyrin metabolism pathway. Interestingly, our results indicate that the lexA regulon in Salmonella, which partially mediates the response to DNA damage, may contain only 60% of the genes present in this regulon in E. coli. In addition, nanH was found to be highly induced by MX and contains a putative lexA regulatory motif in its regulatory region, suggesting that it may be regulated by lexA. CONCLUSION: Operon and monotonic analyses improved the determination of differentially expressed genes beyond that of Bayesian-t analysis, showing that MX alters cellular metabolism involving pathways other than DNA damage. Because co-expression of similarly functioning genes also occurs in eukaryotes, this method has general applicability for improving analysis of toxicogenomic data. [Abstract/Link to Full Text]

Hoehndorf R, Loebe F, Kelso J, Herre H
Representing default knowledge in biomedical ontologies: Application to the integration of anatomy and phenotype ontologies.
BMC Bioinformatics. 2007 Oct 9;8(1):377.
ABSTRACT: BACKGROUND: Current efforts within the biomedical ontology community focus on achieving interoperability between various biomedical ontologies that cover a range of diverse domains. Achieving this interoperability will contribute to the creation of a rich knowledge base that can be used for querying, as well as generating and testing novel hypotheses. The OBO Foundry principles, as applied to a number of biomedical ontologies, are designed to facilitate this interoperability. However, semantic extensions are required to meet the OBO Foundry interoperability goals. Inconsistencies may arise when ontologies of properties - mostly phenotype ontologies - are combined with ontologies taking a canonical view of a domain - such as many anatomical ontologies. Currently, there is no support for a correct and consistent integration of such ontologies. RESULTS: We have developed a methodology for accurately representing canonical domain ontologies within the OBO Foundry. This is achieved by adding an extension to the semantics for relationships in the biomedical ontologies that allows for treating canonical information as default. Conclusions drawn from default knowledge may be revoked when additional information becomes available. We show how this extension can be used to achieve interoperability between ontologies, and further allows for the inclusion of more knowledge within them. We apply the formalism to ontologies of mouse anatomy and mammalian phenotypes in order to demonstrate the approach. CONCLUSION: Biomedical ontologies require a new class of relations that can be used in conjunction with default knowledge, thereby extending those currently in use. The inclusion of default knowledge is necessary in order to ensure interoperability between ontologies. [Abstract/Link to Full Text]

Lipniacki T, Puszynski K, Paszek P, Brasier AR, Kimmel M
Single TNFalpha trimers mediating NF-kappaB activation: Stochastic robustness of NF-kappaB signaling.
BMC Bioinformatics. 2007 Oct 9;8(1):376.
ABSTRACT: BACKGROUND: The NF-kappaB regulatory network controls innate immune response by transducing variety of pathogen-derived and cytokine stimuli into well defined single-cell gene regulatory events. RESULTS: We analyze the network by means of the model combining a deterministic description for molecular species with large cellular concentrations with two classes of stochastic switches: cell-surface receptor activation by TNFalpha ligand, and IkappaBalpha and A20 genes activation by NF-kappaB molecules. Both stochastic switches are associated with amplification pathways capable of translating single molecular events into tens of thousands of synthesized or degraded proteins. Here, we show that at a low TNFalpha dose only a fraction of cells are activated, but in these activated cells the amplification mechanisms assure that the amplitude of NF-kappaB nuclear translocation remains above a threshold. Similarly, the lower nuclear NF-kappaB concentration only reduces the probability of gene activation, but does not reduce gene expression of those responding. CONCLUSION: These two effects provide a particular stochastic robustness in cell regulation, allowing cells to respond differently to the same stimuli, but causing their individual responses to be unequivocal. Both effects are likely to be crucial in the early immune response: Diversity in cell responses causes that the tissue defense is harder to overcome by relatively simple programs coded in viruses and other pathogens. The more focused single-cell responses help cells to choose their individual fates such as apoptosis or proliferation. The model supports the hypothesis that binding of single TNFalpha ligands is sufficient to induce massive NF-kappaB translocation and activation of NF-kappaB dependent genes. [Abstract/Link to Full Text]

Jiang B, Qu H, Hu Y, Ni T, Lin Z
Computational analysis of the relationship between allergenicity and digestibility of allergenic proteins in simulated gastric fluid.
BMC Bioinformatics. 2007;8375.
BACKGROUND: Safety assessment of genetically modified (GM) food, with regard to allergenic potential of transgene-encoded xenoproteins, typically involves several different methods, evaluation by digestibility being one thereof. However, there are still debates about whether the allergenicity of food allergens is related to their resistance to digestion by the gastric fluid. The disagreements may in part stem from classification of allergens only by their sources, which we believe is inadequate, and the difficulties in achieving identical experimental conditions for studying digestion by simulated gastric fluid (SGF) so that results can be compared. Here, we reclassify allergenic food allergens into alimentary canal-sensitized (ACS) and non-alimentary canal-sensitized (NACS) allergens and use a computational model that simulates gastric fluid digestion to analyze the digestibilities of these two types. RESULTS: The model presented in this paper is as effective as SGF digestion experiments, but more stable and reproducible. On the basis of this model, food allergens are satisfactorily classified as ACS and NACS types by their pathways for sensitization; the former are relatively resistant to gastric fluid digestion while the later are relatively labile. CONCLUSION: The results suggest that it is better to classify allergens into ACS and NACS types when understanding the relationship between their digestibility and allergenicity and the digestibility of a target foreign protein is a parameter for evaluating its allergenicity during safety assessments of GM food. [Abstract/Link to Full Text]

Fan X, Zhu J, Schadt EE, Liu JS
Statistical power of phylo-HMM for evolutionarily conserved element detection.
BMC Bioinformatics. 2007 Oct 5;8(1):374.
ABSTRACT: BACKGROUND: An important goal of comparative genomics is the identification of functional elements through conservation analysis. Phylo-HMM was recently introduced to detect conserved elements based on multiple genome alignments, but the method has not been rigorously evaluated. RESULTS: We report here a simulation study to investigate the power of phylo-HMM. We show that the power of the phylo-HMM approach depends on many factors, among which the most important are the number of species-specific genomes used and evolutionary distances between pairs of species. This finding is consistent with results reported by other groups for simpler comparative genomics models. In addition, the conservation ratio of conserved elements and the expected length of the conserved elements are also major factors. In contrast, the influence of the topology and the nucleotide substitution model are relatively minor. CONCLUSIONS: Our results give general rules about how to select the number of genomes and their revolutionary distance in comparative genomics studies, and what level of power we can expect under different parameter settings. [Abstract/Link to Full Text]

Gabdoulline RR, Stein M, Wade RC
qPIPSA: Relating enzymatic kinetic parameters and interaction fields.
BMC Bioinformatics. 2007 Oct 5;8(1):373.
ABSTRACT: BACKGROUND: The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computational methods to estimate these parameters are needed. It is possible to use the three-dimensional structure of an enzyme to perform simulations of a reaction and derive kinetic parameters. However, this is computationally demanding and requires detailed knowledge of the enzyme mechanism. We have therefore sought to develop a general, simple and computationally efficient procedure to relate protein structural information to enzymatic kinetic parameters that allows consistency between the kinetic and structural information to be checked and estimation of kinetic constants for structurally and mechanistically similar enzymes. RESULTS: We describe qPIPSA: quantitative Protein Interaction Property Similarity Analysis. In this analysis, molecular interaction fields, for example, electrostatic potentials, are computed from the enzyme structures. Differences in molecular interaction fields between enzymes are then related to the ratios of their kinetic parameters. This procedure can be used to estimate unknown kinetic parameters when enzyme structural information is available and kinetic parameters have been measured for related enzymes or were obtained under different conditions. The detailed interaction of the enzyme with substrate or cofactors is not modeled and is assumed to be similar for all the proteins compared. The protein structure modeling protocol employed ensures that differences between models reflect genuine differences between the protein sequences, rather than random fluctuations in protein structure. CONCLUSIONS: Provided that the experimental conditions and the protein structural models refer to the same protein state or conformation, correlations between interaction fields and kinetic parameters can be established for sets of related enzymes. Outliers may arise due to variation in the importance of different contributions to the kinetic parameters, such as protein stability and conformational changes. The qPIPSA approach can assist in the validation as well as estimation of kinetic parameters, and provide insights into enzyme mechanism. [Abstract/Link to Full Text]

Berger SI, Posner JM, Ma'ayan A
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases.
BMC Bioinformatics. 2007;8372.
BACKGROUND: In recent years, mammalian protein-protein interaction network databases have been developed. The interactions in these databases are either extracted manually from low-throughput experimental biomedical research literature, extracted automatically from literature using techniques such as natural language processing (NLP), generated experimentally using high-throughput methods such as yeast-2-hybrid screens, or interactions are predicted using an assortment of computational approaches. Genes or proteins identified as significantly changing in proteomic experiments, or identified as susceptibility disease genes in genomic studies, can be placed in the context of protein interaction networks in order to assign these genes and proteins to pathways and protein complexes. RESULTS: Genes2Networks is a software system that integrates the content of ten mammalian interaction network datasets. Filtering techniques to prune low-confidence interactions were implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from "seed" lists of human Entrez gene symbols. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. CONCLUSION: Genes2Networks is powerful web-based software that can help experimental biologists to interpret lists of genes and proteins such as those commonly produced through genomic and proteomic experiments, as well as lists of genes and proteins associated with disease processes. This system can be used to find relationships between genes and proteins from seed lists, and predict additional genes or proteins that may play key roles in common pathways or protein complexes. [Abstract/Link to Full Text]

Kerr KF
Extended analysis of benchmark datasets for Agilent two-color microarrays.
BMC Bioinformatics. 2007 Oct 3;8(1):371.
ABSTRACT: BACKGROUND: As part of its broad and ambitious mission, the MicroArray Quality Control (MAQC) project reported the results of experiments using External RNA Controls (ERCs) on five microarray platforms. For most platforms, several different methods of data processing were considered. However, there was no similar consideration of different methods for processing the data from the Agilent two-color platform. While this omission is understandable given the scale of the project, it can create the false impression that there is consensus about the best way to process Agilent two-color data. It is also important to consider whether ERCs are representative of all the probes on a microarray. RESULTS: A comparison of different methods of processing Agilent two-color data shows substantial differences among methods for low-intensity genes. The sensitivity and specificity for detecting differentially expressed genes varies substantially for different methods. Analysis also reveals that the ERCs in the MAQC data only span the upper half of the intensity range, and therefore cannot be representative of all genes on the microarray. CONCLUSIONS: Although ERCs demonstrate good agreement between observed and expected log-ratios on the Agilent two-color platform, such an analysis is incomplete. Simple loess normalization outperformed data processing with Agilent's Feature Extraction software for accurate identification of differentially expressed genes. Results from studies using ERCs should not be over-generalized when ERCs are not representative of all probes on a microarray. [Abstract/Link to Full Text]

Zhang JG, Deng HW
Gene selection for classification of microarray data based on the Bayes error.
BMC Bioinformatics. 2007;8(1):370.
ABSTRACT: BACKGROUND: With DNA microarray data, selecting a compact subset of discriminative genes from thousands of genes is a critical step for accurate classification of phenotypes for, e.g., disease diagnosis. Several widely used gene selection methods often select top-ranked genes according to their individual discriminative power in classifying samples into distinct categories, without considering correlations among genes. A limitation of these gene selection methods is that they may result in gene sets with some redundancy and yield an unnecessary large number of candidate genes for classification analyses. Some latest studies show that incorporating gene to gene correlations into gene selection can remove redundant genes and improve classification accuracy. RESULTS: In this study, we propose a new method, Based Bayes error Filter (BBF), to select relevant genes and remove redundant genes in classification analyses of microarray data. The effectiveness and accuracy of this method is demonstrated through analyses of five publicly available microarray datasets. The results show that our gene selection method is capable of achieving better accuracies than previous studies, while being able to effectively select relevant genes, remove redundant genes and obtain efficient and small gene sets for sample classification purposes. CONCLUSION: The proposed method can effectively identify a compact set of genes with high classification accuracy. This study also indicates that application of the Bayes error is a feasible and effective wayfor removing redundant genes in gene selection. [Abstract/Link to Full Text]

Fredslund J, Lange M
Primique: automatic design of specific PCR primers for each sequence in a family.
BMC Bioinformatics. 2007;8369.
BACKGROUND: In many contexts, researchers need specific primers for all sequences in a family such that each primer set amplifies only its target sequence and none of the others, e.g. to detect which transcription factor out of a family of very similar proteins that is present in a sample, or to design diagnostic assays for the identification of pathogen strains. RESULTS: This paper presents primique, a new graphical, user-friendly, fast, web-based tool which solves the problem: It designs specific primers for each sequence in an uploaded set. Further, a secondary set of sequences not to be amplified by any primer pair may be uploaded. Primers with high sequence similarity to non-target sequences are selected against. Lastly, the suggested primers may be checked against the National Center for Biotechnology Information databases for possible mis-priming. CONCLUSION: Results are presented in interactive tables, and various primer properties are listed and displayed graphically. Any close match alignments can be displayed. Given 30 sequences, the running time of primique is about 20 seconds.primique can be reached via this web address: http://cgi-www.daimi.au.dk/cgi-chili/primique/front.py. [Abstract/Link to Full Text]

Baross A, Delaney AD, Li HI, Nayar T, Flibotte S, Qian H, Chan SY, Asano J, Ally A, Cao M, Birch P, Brown-John M, Fernandes N, Go A, Kennedy G, Langlois S, Eydoux P, Friedman JM, Marra MA
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.
BMC Bioinformatics. 2007 Oct 2;8(1):368.
ABSTRACT: BACKGROUND: Genomic deletions and duplications are important in the pathogenesis of diseases, such as cancer and mental retardation, and have recently been shown to occur frequently in unaffected individuals as polymorphisms. Affymetrix GeneChip whole genome sampling analysis (WGSA) combined with 100K single nucleotide polymorphism (SNP) genotyping arrays is one of several microarray-based approaches that are now being used to detect such structural genomic changes. The popularity of this technology and its associated open source data format have resulted in the development of an increasing number of software packages for the analysis of copy number changes using these SNP arrays. RESULTS: We evaluated four publicly available software packages for high throughput copy number analysis using synthetic and empirical 100K SNP array data sets, the latter obtained from 107 mental retardation (MR) patients and their unaffected parents and siblings. We evaluated the software with regards to overall suitability for high-throughput 100K SNP array data analysis, as well as effectiveness of normalization, scaling with various reference sets and feature extraction, as well as true and false positive rates of genomic copy number variant (CNV) detection. CONCLUSION: We observed considerable variation among the numbers and types of candidate CNVs detected by different analysis approaches, and found that multiple programs were needed to find all real aberrations in our test set. The frequency of false positive deletions was substantial, but could be greatly reduced by using the SNP genotype information to confirm loss of heterozygosity. [Abstract/Link to Full Text]

Küntzer J, Backes C, Blum T, Gerasch A, Kaufmann M, Kohlbacher O, Lenhof HP
BNDB - the Biochemical Network Database.
BMC Bioinformatics. 2007;8367.
BACKGROUND: Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources. DESCRIPTION: We present the Biochemical Network Database (BNDB), a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a web interface for the search and curation of the data, a Java-based viewer (BiNA) provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB. CONCLUSION: BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at http://www.bndb.org. [Abstract/Link to Full Text]

Horesh Y, Doniger T, Michaeli S, Unger R
RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules.
BMC Bioinformatics. 2007 Oct 1;8(1):366.
ABSTRACT: BACKGROUND: In recent years, RNA molecules that are not translated into proteins (ncRNAs) have drawn a great deal of attention, as they were shown to be involved in many cellular functions. One of the most important computational problems regarding ncRNA is to predict the secondary structure of a molecule from its sequence. In particular, we attempted to predict the secondary structure for a set of unaligned ncRNA molecules that are taken from the same family, and thus presumably have a similar structure. RESULTS: We developed the RNAspa program, which comparatively predicts the secondary structure for a set of ncRNA molecules in linear time in the number of molecules. We observed that in a list of several hundred suboptimal minimal free energy (MFE) predictions, as provided by the RNAsubopt program of the Vienna package, it is likely that at least one suggested structure would be similar to the true, correct one. The suboptimal solutions of each molecule are represented as a layer of vertices in a graph. The shortest path in this graph is the basis for structural predictions for the molecule. We also show that RNA secondary structures can be compared very rapidly by a simple string Edit-Distance algorithm with a minimal loss of accuracy. We show that this approach allows us to more deeply explore the suboptimal structure space. CONCLUSIONS: The algorithm was tested on two datasets each includes several ncRNA families taken from the Rfam database. These datasets, used in previous studies, allowed for comparison of the algorithm with other methods. In these tests, RNAspa performed better than four other programs. [Abstract/Link to Full Text]

Schlitt T, Brazma A
Current approaches to gene regulatory network modelling.
BMC Bioinformatics. 2007;8 Suppl 6S9.
Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology models, network control logic models, and dynamic models. Here we will describe some examples for each of these categories. We will study the topology of gene regulatory networks in yeast in more detail, comparing a direct network derived from transcription factor binding data and an indirect network derived from genome-wide expression data in mutants. Regarding the network dynamics we briefly describe discrete and continuous approaches to network modelling, then describe a hybrid model called Finite State Linear Model and demonstrate that some simple network dynamics can be simulated in this model. [Abstract/Link to Full Text]

Schlitt T, Brazma A
Modelling gene networks at different organisational levels.
FEBS Lett. 2005 Mar 21;579(8):1859-66.
Approaches to modelling gene regulation networks can be categorized, according to increasing detail, as network parts lists, network topology models, network control logic models, or dynamic models. We discuss the current state of the art for each of these approaches. There is a gap between the parts list and topology models on one hand, and control logic and dynamic models on the other hand. The first two classes of models have reached a genome-wide scale, while for the other model classes high throughput technologies are yet to make a major impact. [Abstract/Link to Full Text]

Schlitt T, Brazma A
Modelling in molecular biology: describing transcription regulatory networks at different scales.
Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29;361(1467):483-94.
Approaches to describe gene regulation networks can be categorized by increasing detail, as network parts lists, network topology models, network control logic models or dynamic models. We discuss the current state of the art for each of these approaches. We study the relationship between different topology models, and give examples how they can be used to infer functional annotations for genes of unknown function. We introduce a new simple way of describing dynamic models called finite state linear model (FSLM). We discuss the gap between the parts list and topology models on one hand, and network logic and dynamic models, on the other hand. The first two classes of models have reached a genome-wide scale, while for the other model classes high-throughput technologies are yet to make a major impact. [Abstract/Link to Full Text]

Huber W, Carey VJ, Long L, Falcon S, Gentleman R
Graphs in molecular biology.
BMC Bioinformatics. 2007;8 Suppl 6S8.
Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of application in molecular biology. We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network. [Abstract/Link to Full Text]

Lässig M
From biophysics to evolutionary genetics: statistical aspects of gene regulation.
BMC Bioinformatics. 2007;8 Suppl 6S7.
This is an introductory review on how genes interact to produce biological functions. Transcriptional interactions involve the binding of proteins to regulatory DNA. Specific binding sites can be identified by genomic analysis, and these undergo a stochastic evolution process governed by selection, mutations, and genetic drift. We focus on the links between the biophysical function and the evolution of regulatory elements. In particular, we infer fitness landscapes of binding sites from genomic data, leading to a quantitative evolutionary picture of regulation. [Abstract/Link to Full Text]

Bussemaker HJ, Ward LD, Boorsma A
Dissecting complex transcriptional responses using pathway-level scores based on prior information.
BMC Bioinformatics. 2007;8 Suppl 6S6.
BACKGROUND: The genomewide pattern of changes in mRNA expression measured using DNA microarrays is typically a complex superposition of the response of multiple regulatory pathways to changes in the environment of the cells. The use of prior information, either about the function of the protein encoded by each gene, or about the physical interactions between regulatory factors and the sequences controlling its expression, has emerged as a powerful approach for dissecting complex transcriptional responses. RESULTS: We review two different approaches for combining the noisy expression levels of multiple individual genes into robust pathway-level differential expression scores. The first is based on a comparison between the distribution of expression levels of genes within a predefined gene set and those of all other genes in the genome. The second starts from an estimate of the strength of genomewide regulatory network connectivities based on sequence information or direct measurements of protein-DNA interactions, and uses regression analysis to estimate the activity of gene regulatory pathways. The statistical methods used are explained in detail. CONCLUSION: By avoiding the thresholding of individual genes, pathway-level analysis of differential expression based on prior information can be considerably more sensitive to subtle changes in gene expression than gene-level analysis. The methods are technically straightforward and yield results that are easily interpretable, both biologically and statistically. [Abstract/Link to Full Text]

Markowetz F, Spang R
Inferring cellular networks--a review.
BMC Bioinformatics. 2007;8 Suppl 6S5.
In this review we give an overview of computational and statistical methods to reconstruct cellular networks. Although this area of research is vast and fast developing, we show that most currently used methods can be organized by a few key concepts. The first part of the review deals with conditional independence models including Gaussian graphical models and Bayesian networks. The second part discusses probabilistic and graph-based methods for data from experimental interventions and perturbations. [Abstract/Link to Full Text]

van Nimwegen E
Finding regulatory elements and regulatory motifs: a general probabilistic framework.
BMC Bioinformatics. 2007;8 Suppl 6S4.
Over the last two decades a large number of algorithms has been developed for regulatory motif finding. Here we show how many of these algorithms, especially those that model binding specificities of regulatory factors with position specific weight matrices (WMs), naturally arise within a general Bayesian probabilistic framework. We discuss how WMs are constructed from sets of regulatory sites, how sites for a given WM can be discovered by scanning of large sequences, how to cluster WMs, and more generally how to cluster large sets of sites from different WMs into clusters. We discuss how 'regulatory modules', clusters of sites for subsets of WMs, can be found in large intergenic sequences, and we discuss different methods for ab initio motif finding, including expectation maximization (EM) algorithms, and motif sampling algorithms. Finally, we extensively discuss how module finding methods and ab initio motif finding methods can be extended to take phylogenetic relations between the input sequences into account, i.e. we show how motif finding and phylogenetic footprinting can be integrated in a rigorous probabilistic framework. The article is intended for readers with a solid background in applied mathematics, and preferably with some knowledge of general Bayesian probabilistic methods. The main purpose of the article is to elucidate that all these methods are not a disconnected set of individual algorithmic recipes, but that they are just different facets of a single integrated probabilistic theory. [Abstract/Link to Full Text]

Zhang MQ
Computational analyses of eukaryotic promoters.
BMC Bioinformatics. 2007;8 Suppl 6S3.
Computational analysis of eukaryotic promoters is one of the most difficult problems in computational genomics and is essential for understanding gene expression profiles and reverse-engineering gene regulation network circuits. Here I give a basic introduction of the problem and recent update on both experimental and computational approaches. More details may be found in the extended references. This review is based on a summer lecture given at Max Planck Institute at Berlin in 2005. [Abstract/Link to Full Text]

Sperling S
Transcriptional regulation at a glance.
BMC Bioinformatics. 2007;8 Suppl 6S2.
Considering that 80 genomes have been sequenced, providing us with the static information of the genome, it is still a long way to reveal the relationship between complex genotypes and phenotypes. The transcriptional regulation process is one of the obstacles that need to be understood to bridge our current information gap. It describes the first step from the genomic sequence information to RNA templates used for protein production or as direct functional units, like non-coding RNAs (e.g. micro RNAs). This introduction aims to highlight the key aspects of the transcriptional process from our current understanding. [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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Blystone B
WWW.Cell Biology Education.
Cell Biol Educ. 2002;1(1):9. [Abstract/Link to Full Text]

Bruns PJ
HHMI: educating tomorrow's scientists.
Cell Biol Educ. 2002;1(1):10. [Abstract/Link to Full Text]

Allen D, Tanner K
Approaches in cell biology teaching.
Cell Biol Educ. 2002;1(1):3-5. [Abstract/Link to Full Text]

Guziewicz M, Vitullo T, Simmons B, Kohn RE
Analyzing defects in the Caenorhabditis elegans nervous system using organismal and cell biological approaches.
Cell Biol Educ. 2002;1(1):18-25.
The goal of this laboratory exercise is to increase student understanding of the impact of nervous system function at both the organismal and cellular levels. This inquiry-based exercise is designed for an undergraduate course examining principles of cell biology. After observing the movement of Caenorhabditis elegans with defects in their nervous system, students examine the structure of the nervous system to categorize the type of defect. They distinguish between defects in synaptic vesicle transport and defects in synaptic vesicle fusion with membranes. The synaptic vesicles are tagged with green fluorescent protein (GFP), simplifying cellular analysis. The expected outcome of this experiment is that students will better understand the concepts of vesicle transport, neurotransmitter release, GFP, and the relation between the nervous system and behavior. [Abstract/Link to Full Text]

Wood WB
Genesis of biochemistry: a problems approach.
Cell Biol Educ. 2002;1(1):16-7. [Abstract/Link to Full Text]

Allen D, Tanner K
Approaches to cell biology teaching: questions about questions.
Cell Biol Educ. 2002;1(3):63-7. [Abstract/Link to Full Text]

Ledbetter ML, Lippert MJ
Glucose transport in cultured animal cells: an exercise for the undergraduate cell biology laboratory.
Cell Biol Educ. 2002;1(3):76-86.
Membrane transport is a fundamental concept that undergraduate students of cell biology understand better with laboratory experience. Formal teaching exercises commonly used to illustrate this concept are unbiological, qualitative, or intricate and time consuming to prepare. We have developed an exercise that uses uptake of radiolabeled nutrient analogues by attachment-dependent animal cells cultured on multiwell trays. This system can readily be manipulated within a typical 3-h laboratory period to yield reproducible, biologically relevant, quantitative data regarding key aspects of membrane transport. Each 24-well tray of cultures allows a group of two to four students to compare eight conditions in triplicate. If different groups of students test different conditions or different types of cells, data can be shared for an even broader experience. The exercise is also readily adaptable for open-ended student projects. Here we illustrate the exercise measuring uptake of the nonmetabolizable glucose analogue [(3)H]-2-deoxy-D-glucose. Students successfully tested the effects of competing sugars, putative inhibitors of the GLUT1 transporter, and changes in cell physiology that might be expected to affect glucose transport in epithelial cells and fibroblasts. In this exercise students find the nutritional and medical implications of glucose transport and its regulation intriguing. They also learn to handle radioisotopes and cultured cells. [Abstract/Link to Full Text]

Dancy MH, Beichner RJ
But are they learning? Getting started in classroom evaluation.
Cell Biol Educ. 2002;1(3):87-94.
There are increasing numbers of traditional biologists, untrained in educational research methods, who want to develop and assess new classroom innovations. In this article we argue the necessity of formal research over normal classroom feedback. We also argue that traditionally trained biologists can make significant contributions to biology pedagogy. We then offer some guidance to the biologist with no formal educational research training who wants to get started. Specifically, we suggest ways to find out what others have done, we discuss the difference between qualitative and quantitative research, and we elaborate on the process of gaining insights from student interviews. We end with an example of a project that has used many different research techniques. [Abstract/Link to Full Text]

Campbell AM
Meeting report: genomics in the undergraduate curriculum--rocket science or basic science?
Cell Biol Educ. 2002;1(3):70-2. [Abstract/Link to Full Text]

Blystone B
WWW.Cell Biology Education.
Cell Biol Educ. 2002;1(3):68-9. [Abstract/Link to Full Text]

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Recent Articles in BMC Medical Informatics and Decision Making

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Dong P, Wong LL, Ng S, Loh M, Mondry A
Quantitative evaluation of recall and precision of CAT Crawler, a search engine specialized on retrieval of Critically Appraised Topics.
BMC Med Inform Decis Mak. 2004 Dec 10;4(1):21.
BACKGROUND: Critically Appraised Topics (CATs) are a useful tool that helps physicians to make clinical decisions as the healthcare moves towards the practice of Evidence-Based Medicine (EBM). The fast growing World Wide Web has provided a place for physicians to share their appraised topics online, but an increasing amount of time is needed to find a particular topic within such a rich repository. METHODS: A web-based application, namely the CAT Crawler, was developed by Singapore's Bioinformatics Institute to allow physicians to adequately access available appraised topics on the Internet. A meta-search engine, as the core component of the application, finds relevant topics following keyword input. The primary objective of the work presented here is to evaluate the quantity and quality of search results obtained from the meta-search engine of the CAT Crawler by comparing them with those obtained from two individual CAT search engines. From the CAT libraries at these two sites, all possible keywords were extracted using a keyword extractor. Of those common to both libraries, ten were randomly chosen for evaluation. All ten were submitted to the two search engines individually, and through the meta-search engine of the CAT Crawler. Search results were evaluated for relevance both by medical amateurs and professionals, and the respective recall and precision were calculated. RESULTS: While achieving an identical recall, the meta-search engine showed a precision of 77.26% (+/-14.45) compared to the individual search engines' 52.65% (+/-12.0) (p < 0.001). CONCLUSION: The results demonstrate the validity of the CAT Crawler meta-search engine approach. The improved precision due to inherent filters underlines the practical usefulness of this tool for clinicians. [Abstract/Link to Full Text]

Hembroff LA, Holmes-Rovner M, Wills CE
Treatment decision-making and the form of risk communication: results of a factorial survey.
BMC Med Inform Decis Mak. 2004 Nov 16;420.
BACKGROUND: Prospective users of preventive therapies often must evaluate complex information about therapeutic risks and benefits. The purpose of this study was to evaluate the effect of relative and absolute risk information on patient decision-making in scenarios typical of health information for patients. METHODS: Factorial experiments within a telephone survey of the Michigan adult, non-institutionalized, English-speaking population. Average interview lasted 23 minutes. Subjects and sample design: 952 randomly selected adults within a random-digit dial sample of Michigan households. Completion rate was 54.3%. RESULTS: When presented hypothetical information regarding additional risks of breast cancer from a medication to prevent a bone disease, respondents reduced their willingness to recommend a female friend take the medication compared to the baseline rate (66.8% = yes). The decrease was significantly greater with relative risk information. Additional benefit information regarding preventing heart disease from the medication increased willingness to recommend the medication to a female friend relative to the baseline scenario, but did not differ between absolute and relative risk formats. When information about both increased risk of breast cancer and reduced risk of heart disease were provided, typical respondents appeared to make rational decisions consistent with Expected Utility Theory, but the information presentation format affected choices. Those 11% - 33% making decisions contrary to the medical indications were more likely to be Hispanic, older, more educated, smokers, and to have children in the home. CONCLUSIONS: In scenarios typical of health risk information, relative risk information led respondents to make non-normative decisions that were "corrected" when the frame used absolute risk information. This population sample made generally rational decisions when presented with absolute risk information, even in the context of a telephone interview requiring remembering rates given. The lack of effect of gender and race suggests that a standard strategy of presenting absolute risk information may improve patient decision-making. [Abstract/Link to Full Text]

Pantazi SV, Arocha JF, Moehr JR
Case-based medical informatics.
BMC Med Inform Decis Mak. 2004 Nov 8;4(1):19.
BACKGROUND: The "applied" nature distinguishes applied sciences from theoretical sciences. To emphasize this distinction, we begin with a general, meta-level overview of the scientific endeavor. We introduce the knowledge spectrum and four interconnected modalities of knowledge. In addition to the traditional differentiation between implicit and explicit knowledge we outline the concepts of general and individual knowledge. We connect general knowledge with the "frame problem," a fundamental issue of artificial intelligence, and individual knowledge with another important paradigm of artificial intelligence, case-based reasoning, a method of individual knowledge processing that aims at solving new problems based on the solutions to similar past problems.We outline the fundamental differences between Medical Informatics and theoretical sciences and propose that Medical Informatics research should advance individual knowledge processing (case-based reasoning) and that natural language processing research is an important step towards this goal that may have ethical implications for patient-centered health medicine. DISCUSSION: We focus on fundamental aspects of decision-making, which connect human expertise with individual knowledge processing. We continue with a knowledge spectrum perspective on biomedical knowledge and conclude that case-based reasoning is the paradigm that can advance towards personalized healthcare and that can enable the education of patients and providers.We center the discussion on formal methods of knowledge representation around the frame problem. We propose a context-dependent view on the notion of "meaning" and advocate the need for case-based reasoning research and natural language processing. In the context of memory based knowledge processing, pattern recognition, comparison and analogy-making, we conclude that while humans seem to naturally support the case-based reasoning paradigm (memory of past experiences of problem-solving and powerful case matching mechanisms), technical solutions are challenging.Finally, we discuss the major challenges for a technical solution: case record comprehensiveness, organization of information on similarity principles, development of pattern recognition and solving ethical issues. SUMMARY: Medical Informatics is an applied science that should be committed to advancing patient-centered medicine through individual knowledge processing. Case-based reasoning is the technical solution that enables a continuous individual knowledge processing and could be applied providing that challenges and ethical issues arising are addressed appropriately. [Abstract/Link to Full Text]

Laerum H, Karlsen TH, Faxvaag A
Use of and attitudes to a hospital information system by medical secretaries, nurses and physicians deprived of the paper-based medical record: a case report.
BMC Med Inform Decis Mak. 2004 Oct 16;418.
BACKGROUND: Most hospitals keep and update their paper-based medical records after introducing an electronic medical record or a hospital information system (HIS). This case report describes a HIS in a hospital where the paper-based medical records are scanned and eliminated. To evaluate the HIS comprehensively, the perspectives of medical secretaries and nurses are described as well as that of physicians. METHODS: We have used questionnaires and interviews to assess and compare frequency of use of the HIS for essential tasks, task performance and user satisfaction among medical secretaries, nurses and physicians. RESULTS: The medical secretaries use the HIS much more than the nurses and the physicians, and they consider that the electronic HIS greatly has simplified their work. The work of nurses and physicians has also become simplified, but they find less satisfaction with the system, particularly with the use of scanned document images. CONCLUSIONS: Although the basis for reference is limited, the results support the assertion that replacing the paper-based medical record primarily benefits the medical secretaries, and to a lesser degree the nurses and the physicians. The varying results in the different employee groups emphasize the need for a multidisciplinary approach when evaluating a HIS. [Abstract/Link to Full Text]

Kline JA, Johnson CL, Webb WB, Runyon MS
Prospective study of clinician-entered research data in the Emergency Department using an Internet-based system after the HIPAA Privacy Rule.
BMC Med Inform Decis Mak. 2004 Oct 12;417.
BACKGROUND: Design and test the reliability of a web-based system for multicenter, real-time collection of data in the emergency department (ED), under waiver of authorization, in compliance with HIPAA. METHODS: This was a phase I, two-hospital study of patients undergoing evaluation for possible pulmonary embolism. Data were collected by on-duty clinicians on an HTML data collection form (prospective e-form), populated using either a personal digital assistant (PDA) or personal computer (PC). Data forms were uploaded to a central, offsite server using secure socket protocol transfer. Each form was assigned a unique identifier, and all PHI data were encrypted, but were password-accessible by authorized research personnel to complete a follow-up e-form. RESULTS: From April 15, 2003-April 15 2004, 1022 prospective e-forms and 605 follow-up e-forms were uploaded. Complexities of PDA use compelled clinicians to use PCs in the ED for data entry for most forms. No data were lost and server log query revealed no unauthorized entry. Prospectively obtained PHI data, encrypted upon server upload, were successfully decrypted using password-protected access to allow follow-up without difficulty in 605 cases. Non-PHI data from prospective and follow-up forms were available to the study investigators via standard file transfer protocol. CONCLUSIONS: Data can be accurately collected from on-duty clinicians in the ED using real-time, PC-Internet data entry in compliance with the Privacy Rule. Deidentification-reidentification of PHI was successfully accomplished by a password-protected encryption-deencryption mechanism to permit follow-up by approved research personnel. [Abstract/Link to Full Text]

Berman JJ
Doublet method for very fast autocoding.
BMC Med Inform Decis Mak. 2004 Sep 15;416.
BACKGROUND: Autocoding (or automatic concept indexing) occurs when a software program extracts terms contained within text and maps them to a standard list of concepts contained in a nomenclature. The purpose of autocoding is to provide a way of organizing large documents by the concepts represented in the text. Because textual data accumulates rapidly in biomedical institutions, the computational methods used to autocode text must be very fast. The purpose of this paper is to describe the doublet method, a new algorithm for very fast autocoding. METHODS: An autocoder was written that transforms plain-text into intercalated word doublets (e.g. "The ciliary body produces aqueous humor" becomes "The ciliary, ciliary body, body produces, produces aqueous, aqueous humor"). Each doublet is checked against an index of doublets extracted from a standard nomenclature. Matching doublets are assigned a numeric code specific for each doublet found in the nomenclature. Text doublets that do not match the index of doublets extracted from the nomenclature are not part of valid nomenclature terms. Runs of matching doublets from text are concatenated and matched against nomenclature terms (also represented as runs of doublets). RESULTS: The doublet autocoder was compared for speed and performance against a previously published phrase autocoder. Both autocoders are Perl scripts, and both autocoders used an identical text (a 170+ Megabyte collection of abstracts collected through a PubMed search) and the same nomenclature (neocl.xml, containing over 102,271 unique names of neoplasms). In side-by-side comparison on the same computer, the doublet method autocoder was 8.4 times faster than the phrase autocoder (211 seconds versus 1,776 seconds). The doublet method codes 0.8 Megabytes of text per second on a desktop computer with a 1.6 GHz processor. In addition, the doublet autocoder successfully matched terms that were missed by the phrase autocoder, while the phrase autocoder found no terms that were missed by the doublet autocoder. CONCLUSIONS: The doublet method of autocoding is a novel algorithm for rapid text autocoding. The method will work with any nomenclature and will parse any ascii plain-text. An implementation of the algorithm in Perl is provided with this article. The algorithm, the Perl implementation, the neoplasm nomenclature, and Perl itself, are all open source materials. [Abstract/Link to Full Text]

Darmoni SJ, Dahamna B, Roth-Berghofer TR
Seal of transparency heritage in the CISMeF quality-controlled health gateway.
BMC Med Inform Decis Mak. 2004 Sep 14;415.
BACKGROUND: It is an absolute necessity to continually assess the quality of health information on the Internet. Quality-controlled subject gateways are Internet services which apply a selected set of targeted measures to support systematic resource discovery. METHODS: The CISMeF health gateway became a contributor to the MedCIRCLE project to evaluate 270 health information providers. The transparency heritage consists of using the evaluation performed on providers that are referenced in the CISMeF catalogue for evaluating the documents they publish, thus passing on the transparency label from the publishers to their documents. RESULTS: Each site rated in CISMeF has a record in the CISMeF database that generates an RDF into HTML file. The search tool Doc'CISMeF displays information originating from every publisher evaluated with a specific MedCIRCLE button, which is linked to the MedCIRCLE central repository. Starting with 270 websites, this trust heritage has led to 6,480 evaluated resources in CISMeF (49.8% of the 13,012 resources included in CISMeF). CONCLUSION: With the MedCIRCLE project and transparency heritage, CISMeF became an explicit third party. [Abstract/Link to Full Text]

Tracy CS, Dantas GC, Upshur RE
Feasibility of a patient decision aid regarding disclosure of personal health information: qualitative evaluation of the Health Care Information Directive.
BMC Med Inform Decis Mak. 2004 Sep 10;413.
BACKGROUND: Concerns regarding the privacy of health information are escalating owing both to the growing use of information technology to store and exchange data and to the increasing demand on the part of patients to control the use of their medical records. The objective of this study was to evaluate the Health Care Information Directive (HCID), a recently-developed patient decision aid that aims to delineate the level of health information an individual is willing to share. METHODS: We convened a series of four focus group meetings with several communities in a large Canadian city. A total of 28 men and women participated, representing health care consumer advocates, urban professionals, senior citizens, and immigrants who speak English as a second language. Data were analysed using qualitative methods. RESULTS: Participants lacked substantial knowledge regarding the fate and uses of personal health information. They expressed mistrust concerning how their information will be used and protected. Several suggestions were made towards customizing the use of data according to specific needs rather than broad and full access to their charts. Furthermore, despite concern regarding the implementation of a tool like the HCID, participants were hopeful that a refined instrument could contribute to the improved regulation of health information. CONCLUSION: This study indicated poor knowledge concerning the uses of personal health information, distrust concerning security provisions, and cautious support for a patient decision aid such as the HCID to improve control over health data. [Abstract/Link to Full Text]

Johnson AM, Vernon PA, Almeida QJ, Grantier LL, Singarayer R, Jog MS
Screening for Parkinson's disease with response time batteries: a pilot study.
BMC Med Inform Decis Mak. 2004 Sep 13;414.
BACKGROUND: Although significant response time deficits (both reaction time and movement time) have been identified in numerous studies of patients with Parkinson's disease (PD), few attempts have been made to evaluate the use of these measures in screening for PD. METHODS: Receiver operator characteristic curves were used to identify cutoff scores for a unit-weighted composite of two choice response tasks in a sample of 40 patients and 40 healthy participants. These scores were then cross-validated in an independent sample of 20 patients and 20 healthy participants. RESULTS: The unit-weighted movement time composite demonstrated high sensitivity (90%) and specificity (90%) in the identification of PD. Movement time was also significantly correlated (r = 0.59, p < 0.025) with the motor score of the Unified Parkinson's Disease Rating Scale (UPDRS). CONCLUSIONS: Measures of chronometric speed, assessed without the use of biomechanically complex movements, have a potential role in screening for PD. Furthermore, the significant correlation between movement time and UPDRS motor score suggests that movement time may be useful in the quantification of PD severity. [Abstract/Link to Full Text]

Chen D, Soong SJ, Grimes GJ, Orthner HF
Wireless local area network in a prehospital environment.
BMC Med Inform Decis Mak. 2004 Aug 31;412.
BACKGROUND: Wireless local area networks (WLANs) are considered the next generation of clinical data network. They open the possibility for capturing clinical data in a prehospital setting (e.g., a patient's home) using various devices, such as personal digital assistants, laptops, digital electrocardiogram (EKG) machines, and even cellular phones, and transmitting the captured data to a physician or hospital. The transmission rate is crucial to the applicability of the technology in the prehospital setting. METHODS: We created two separate WLANs to simulate a virtual local are network environment such as in a patient's home or an emergency room (ER). The effects of different methods of data transmission, number of clients, and roaming among different access points on the file transfer rate were determined. RESULTS: The present results suggest that it is feasible to transfer small files such as patient demographics and EKG data from the patient's home to the ER at a reasonable speed. Encryption, user control, and access control were implemented and results discussed. CONCLUSIONS: Implementing a WLAN in a centrally managed and multiple-layer-controlled access control server is the key to ensuring its security and accessibility. Future studies should focus on product capacity, speed, compatibility, interoperability, and security management. [Abstract/Link to Full Text]

McKibbon KA, Gadd CS
A quantitative analysis of qualitative studies in clinical journals for the 2000 publishing year.
BMC Med Inform Decis Mak. 2004 Jul 22;411.
BACKGROUND: Quantitative studies are becoming more recognized as important to understanding health care with all of its richness and complexities. The purpose of this descriptive survey was to provide a quantitative evaluation of the qualitative studies published in 170 core clinical journals for 2000. METHODS: All identified studies that used qualitative methods were reviewed to ascertain which clinical journals publish qualitative studies and to extract research methods, content (persons and health care issues studied), and whether mixed methods (quantitative and qualitative methods) were used. RESULTS: 60 330 articles were reviewed. 355 reports of original qualitative studies and 12 systematic review articles were identified in 48 journals. Most of the journals were in the discipline of nursing. Only 4 of the most highly cited health care journals, based on ISI Science Citation Index (SCI) Impact Factors, published qualitative studies. 37 of the 355 original reports used both qualitative and quantitative (mixed) methods. Patients and non-health care settings were the most common groups of people studied. Diseases and conditions were cancer, mental health, pregnancy and childbirth, and cerebrovascular disease with many other diseases and conditions represented. Phenomenology and grounded theory were commonly used; substantial ethnography was also present. No substantial differences were noted for content or methods when articles published in all disciplines were compared with articles published in nursing titles or when studies with mixed methods were compared with studies that included only qualitative methods. CONCLUSIONS: The clinical literature includes many qualitative studies although they are often published in nursing journals or journals with low SCI Impact Factor journals. Many qualitative studies incorporate both qualitative and quantitative methods. [Abstract/Link to Full Text]

Wanger P, Martin L
Algorithms for optimizing drug therapy.
BMC Med Inform Decis Mak. 2004 Jul 20;410.
BACKGROUND: Drug therapy has become increasingly efficient, with more drugs available for treatment of an ever-growing number of conditions. Yet, drug use is reported to be sub optimal in several aspects, such as dosage, patient's adherence and outcome of therapy. The aim of the current study was to investigate the possibility to optimize drug therapy using computer programs, available on the Internet. METHODS: One hundred and ten officially endorsed text documents, published between 1996 and 2004, containing guidelines for drug therapy in 246 disorders, were analyzed with regard to information about patient-, disease- and drug-related factors and relationships between these factors. This information was used to construct algorithms for identifying optimum treatment in each of the studied disorders. These algorithms were categorized in order to define as few models as possible that still could accommodate the identified factors and the relationships between them. The resulting program prototypes were implemented in HTML (user interface) and JavaScript (program logic). RESULTS: Three types of algorithms were sufficient for the intended purpose. The simplest type is a list of factors, each of which implies that the particular patient should or should not receive treatment. This is adequate in situations where only one treatment exists. The second type, a more elaborate model, is required when treatment can by provided using drugs from different pharmacological classes and the selection of drug class is dependent on patient characteristics. An easily implemented set of if-then statements was able to manage the identified information in such instances. The third type was needed in the few situations where the selection and dosage of drugs were depending on the degree to which one or more patient-specific factors were present. In these cases the implementation of an established decision model based on fuzzy sets was required. Computer programs based on one of these three models could be constructed regarding all but one of the studied disorders. The single exception was depression, where reliable relationships between patient characteristics, drug classes and outcome of therapy remain to be defined. CONCLUSION: Algorithms for optimizing drug therapy can, with presumably rare exceptions, be developed for any disorder, using standard Internet programming methods. [Abstract/Link to Full Text]

Churches T, Christen P
Some methods for blindfolded record linkage.
BMC Med Inform Decis Mak. 2004 Jun 28;49.
BACKGROUND: The linkage of records which refer to the same entity in separate data collections is a common requirement in public health and biomedical research. Traditionally, record linkage techniques have required that all the identifying data in which links are sought be revealed to at least one party, often a third party. This necessarily invades personal privacy and requires complete trust in the intentions of that party and their ability to maintain security and confidentiality. Dusserre, Quantin, Bouzelat and colleagues have demonstrated that it is possible to use secure one-way hash transformations to carry out follow-up epidemiological studies without any party having to reveal identifying information about any of the subjects - a technique which we refer to as "blindfolded record linkage". A limitation of their method is that only exact comparisons of values are possible, although phonetic encoding of names and other strings can be used to allow for some types of typographical variation and data errors. METHODS: A method is described which permits the calculation of a general similarity measure, the n-gram score, without having to reveal the data being compared, albeit at some cost in computation and data communication. This method can be combined with public key cryptography and automatic estimation of linkage model parameters to create an overall system for blindfolded record linkage. RESULTS: The system described offers good protection against misdeeds or security failures by any one party, but remains vulnerable to collusion between or simultaneous compromise of two or more parties involved in the linkage operation. In order to reduce the likelihood of this, the use of last-minute allocation of tasks to substitutable servers is proposed. Proof-of-concept computer programmes written in the Python programming language are provided to illustrate the similarity comparison protocol. CONCLUSION: Although the protocols described in this paper are not unconditionally secure, they do suggest the feasibility, with the aid of modern cryptographic techniques and high speed communication networks, of a general purpose probabilistic record linkage system which permits record linkage studies to be carried out with negligible risk of invasion of personal privacy. [Abstract/Link to Full Text]

Berman JJ
Resources for comparing the speed and performance of medical autocoders.
BMC Med Inform Decis Mak. 2004 Jun 15;48.
BACKGROUND: Concept indexing is a popular method for characterizing medical text, and is one of the most important early steps in many data mining efforts. Concept indexing differs from simple word or phrase indexing because concepts are typically represented by a nomenclature code that binds a medical concept to all equivalent representations. A concept search on the term renal cell carcinoma would be expected to find occurrences of hypernephroma, and renal carcinoma (concept equivalents). The purpose of this study is to provide freely available resources to compare speed and performance among different autocoders. These tools consist of: 1) a public domain autocoder written in Perl (a free and open source programming language that installs on any operating system); 2) a nomenclature database derived from the unencumbered subset of the publicly available Unified Medical Language System; 3) a large corpus of autocoded output derived from a publicly available medical text. METHODS: A simple lexical autocoder was written that parses plain-text into a listing of all 1,2,3, and 4-word strings contained in text, assigning a nomenclature code for text strings that match terms in the nomenclature. The nomenclature used is the unencumbered subset of the 2003 Unified Medical Language System (UMLS). The unencumbered subset of UMLS was reduced to exclude homonymous one-word terms and proper names, resulting in a term/code data dictionary containing about a half million medical terms. The Online Mendelian Inheritance in Man (OMIM), a 92+ Megabyte publicly available medical opus, was used as sample medical text for the autocoder. RESULTS: The autocoding Perl script is remarkably short, consisting of just 38 command lines. The 92+ Megabyte OMIM file was completely autocoded in 869 seconds on a 2.4 GHz processor (less than 10 seconds per Megabyte of text). The autocoded output file (9,540,442 bytes) contains 367,963 coded terms from OMIM and is distributed with this manuscript. CONCLUSIONS: A public domain Perl script is provided that can parse through plain-text files of any length, matching concepts against an external nomenclature. The script and associated files can be used freely to compare the speed and performance of autocoding software. [Abstract/Link to Full Text]

Bielli E, Carminati F, La Capra S, Lina M, Brunelli C, Tamburini M
A Wireless Health Outcomes Monitoring System (WHOMS): development and field testing with cancer patients using mobile phones.
BMC Med Inform Decis Mak. 2004 Jun 15;47.
BACKGROUND: Health-Related Quality of Life assessment is widely used in clinical research, but rarely in clinical practice. Barriers including practical difficulties administering printed questionnaires have limited their use. Telehealth technology could reduce these barriers and encourage better doctor-patient interaction regarding patient symptoms and quality-of-life monitoring. The aim of this study was to develop a new system for transmitting patients' self-reported outcomes using mobile phones or the internet, and to test whether patients can and will use the system via a mobile phone. METHODS: We have developed a prototype of a Wireless Health Outcomes Monitoring System, which allows structured questionnaires to be sent to the patient by their medical management team. The patients' answers are directly sent to an authorised website immediately accessible by the medical team, and are displayed in a graphic format that highlights the patient's state of health. In the present study, 97 cancer inpatients were asked to complete a ten-item questionnaire. The questionnaire was delivered by display on a mobile phone, and was answered by the patients using the mobile phone keypad. RESULTS: Of the 97 patients, 56 (58%) attempted the questionnaire, and all of these 56 completed it. Only 6% of the total number of questions were left unanswered by patients. Forty-one (42%) patients refused to participate, mostly due to their lack of familiarity with mobile phone use. Compared with those who completed the questionnaire, patients who refused to participate were older, had fewer years of education and were less familiar with new communications technology (mobile phone calls, mobile phone SMS, internet, email). CONCLUSION: More than half of the patients self-completed the questionnaire using the mobile phone. This proportion may increase with the use of multichannel communications which can be incorporated into the system. The proportion may also increase if the patient's partner and/or family were able to assist the patient with using the technology. These preliminary results encourage further studies to identify specific diseases or circumstances where this system could be useful in patients' distance monitoring. Such a system is likely to detect patient suffering earlier, and to activate a well-timed intervention. [Abstract/Link to Full Text]

Martin C, Vanderpump M, French J
Description and validation of a Markov model of survival for individuals free of cardiovascular disease that uses Framingham risk factors.
BMC Med Inform Decis Mak. 2004 May 24;46.
BACKGROUND: Estimation of cardiovascular disease risk is increasingly used to inform decisions on interventions, such as the use of antihypertensives and statins, or to communicate the risks of smoking. Crude 10-year cardiovascular disease risk risks may not give a realistic view of the likely impact of an intervention over a lifetime and will underestimate of the risks of smoking. A validated model of survival to act as a decision aid in the consultation may help to address these problems. This study aims to describe the development of such a model for use with people free of cardiovascular disease and evaluates its accuracy against data from a United Kingdom cohort. METHODS: A Markov cycle tree evaluated using cohort simulation was developed utilizing Framingham estimates of cardiovascular risk, 1998 United Kingdom mortality data, the relative risk for smoking related non-cardiovascular disease risk and changes in systolic blood pressure and serum total cholesterol total cholesterol with age. The model's estimates of survival at 20 years for 1391 members of the Whickham survey cohort between the ages of 35 and 65 were compared with the observed survival at 20-year follow-up. RESULTS: The model estimate for survival was 75% and the observed survival was 75.4%. The correlation between estimated and observed survival was 0.933 over 39 subgroups of the cohort stratified by estimated survival, 0.992 for the seven 5-year age bands from 35 to 64, 0.936 for the ten 10 mmHg systolic blood pressure bands between 100 mmHg and 200 mmHg, and 0.693 for the fifteen 0.5 mmol/l total cholesterol bands between 3.0 and 10.0 mmol/l. The model significantly underestimated mortality in those people with a systolic blood pressure greater than or equal to 180 mmHg (p = 0.006).The average gain in life expectancy from the elimination of cardiovascular disease risk as a cause of death was 4.0 years for all the 35 year-old men in the sample (n = 24), and 1.8 years for all the 35 year-old women in the sample (n = 32). CONCLUSIONS: This model accurately estimates 20-year survival in subjects from the Whickham cohort with a systolic blood pressure below 180 mmHg. [Abstract/Link to Full Text]

Maglogiannis IG, Zafiropoulos EP
Characterization of digital medical images utilizing support vector machines.
BMC Med Inform Decis Mak. 2004 Mar 10;44.
BACKGROUND: In this paper we discuss an efficient methodology for the image analysis and characterization of digital images containing skin lesions using Support Vector Machines and present the results of a preliminary study. METHODS: The methodology is based on the support vector machines algorithm for data classification and it has been applied to the problem of the recognition of malignant melanoma versus dysplastic naevus. Border and colour based features were extracted from digital images of skin lesions acquired under reproducible conditions, using basic image processing techniques. Two alternative classification methods, the statistical discriminant analysis and the application of neural networks were also applied to the same problem and the results are compared. RESULTS: The SVM (Support Vector Machines) algorithm performed quite well achieving 94.1% correct classification, which is better than the performance of the other two classification methodologies. The method of discriminant analysis classified correctly 88% of cases (71% of Malignant Melanoma and 100% of Dysplastic Naevi), while the neural networks performed approximately the same. CONCLUSION: The use of a computer-based system, like the one described in this paper, is intended to avoid human subjectivity and to perform specific tasks according to a number of criteria. However the presence of an expert dermatologist is considered necessary for the overall visual assessment of the skin lesion and the final diagnosis. [Abstract/Link to Full Text]

Najmi AH, Magruder SF
Estimation of hospital emergency room data using OTC pharmaceutical sales and least mean square filters.
BMC Med Inform Decis Mak. 2004 Mar 15;45.
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 Bioterrorism, has been suggested in the literature. The data streams of interest are quite non-stationary and we address this problem from the viewpoint of linear adaptive filter theory: the clinical data is the primary channel which is to be estimated from the OTC data that form the reference channels. METHOD: The OTC data are grouped into a few categories and we estimate the clinical data using each individual category, as well as using a multichannel filter that encompasses all the OTC categories. The estimation (in the least mean square sense) is performed using an FIR (Finite Impulse Response) filter and the normalized LMS algorithm. RESULTS: We show all estimation results and present a table of effectiveness of each OTC category, as well as the effectiveness of the combined filtering operation. Individual group results clearly show the effectiveness of each particular group in estimating the clinical hospital data and serve as a guide as to which groups have sustained correlations with the clinical data. CONCLUSION: Our results indicate that Multichannel adaptive FIR least squares filtering is a viable means of estimating public health conditions from OTC sales, and provide quantitative measures of time dependent correlations between the clinical data and the OTC data channels. [Abstract/Link to Full Text]

Gissler M, Klemetti R, Sevón T, Hemminki E
Monitoring of IVF birth outcomes in Finland: a data quality study.
BMC Med Inform Decis Mak. 2004 Mar 10;43.
BACKGROUND: The collection of information on infertility treatments is important for the surveillance of potential health consequences and to monitor service provision. STUDY DESIGN: We compared the coverage and outcomes of IVF children reported in aggregated IVF statistics, the Medical Birth Register (subsequently: MBR) and research data based on reimbursements for IVF treatments in Finland in 1996-1998. RESULTS: The number of newborns were nearly equal in the three data sources (N = 4331-4384), but the linkage between the MBR and the research data revealed that almost 40% of the reported IVF children were not the same individuals. The perinatal outcomes in the three data sources were similar, excluding the much lower incidence of major congenital anomalies in the IVF statistics (157/10 000 newborns) compared to other sources (409-422/10 000 newborns). CONCLUSION: The differences in perinatal outcomes in the three data sets were in general minor, which suggests that the observed non-recording in the MBR is most likely unbiased. [Abstract/Link to Full Text]

Dufour JC, Fieschi D, Fieschi M
Coupling computer-interpretable guidelines with a drug-database through a web-based system--The PRESGUID project.
BMC Med Inform Decis Mak. 2004 Mar 2;42.
BACKGROUND: Clinical Practice Guidelines (CPGs) available today are not extensively used due to lack of proper integration into clinical settings, knowledge-related information resources, and lack of decision support at the point of care in a particular clinical context. OBJECTIVE: The PRESGUID project (PREScription and GUIDelines) aims to improve the assistance provided by guidelines. The project proposes an online service enabling physicians to consult computerized CPGs linked to drug databases for easier integration into the healthcare process. METHODS: Computable CPGs are structured as decision trees and coded in XML format. Recommendations related to drug classes are tagged with ATC codes. We use a mapping module to enhance computerized guidelines coupling with a drug database, which contains detailed information about each usable specific medication. In this way, therapeutic recommendations are backed up with current and up-to-date information from the database. RESULTS: Two authoritative CPGs, originally diffused as static textual documents, have been implemented to validate the computerization process and to illustrate the usefulness of the resulting automated CPGs and their coupling with a drug database. We discuss the advantages of this approach for practitioners and the implications for both guideline developers and drug database providers. Other CPGs will be implemented and evaluated in real conditions by clinicians working in different health institutions. [Abstract/Link to Full Text]

Laerum H, Faxvaag A
Task-oriented evaluation of electronic medical records systems: development and validation of a questionnaire for physicians.
BMC Med Inform Decis Mak. 2004 Feb 9;41.
BACKGROUND: Evaluation is a challenging but necessary part of the development cycle of clinical information systems like the electronic medical records (EMR) system. It is believed that such evaluations should include multiple perspectives, be comparative and employ both qualitative and quantitative methods. Self-administered questionnaires are frequently used as a quantitative evaluation method in medical informatics, but very few validated questionnaires address clinical use of EMR systems. METHODS: We have developed a task-oriented questionnaire for evaluating EMR systems from the clinician's perspective. The key feature of the questionnaire is a list of 24 general clinical tasks. It is applicable to physicians of most specialties and covers essential parts of their information-oriented work. The task list appears in two separate sections, about EMR use and task performance using the EMR, respectively. By combining these sections, the evaluator may estimate the potential impact of the EMR system on health care delivery. The results may also be compared across time, site or vendor. This paper describes the development, performance and validation of the questionnaire. Its performance is shown in two demonstration studies (n = 219 and 80). Its content is validated in an interview study (n = 10), and its reliability is investigated in a test-retest study (n = 37) and a scaling study (n = 31). RESULTS: In the interviews, the physicians found the general clinical tasks in the questionnaire relevant and comprehensible. The tasks were interpreted concordant to their definitions. However, the physicians found questions about tasks not explicitly or only partially supported by the EMR systems difficult to answer. The two demonstration studies provided unambiguous results and low percentages of missing responses. In addition, criterion validity was demonstrated for a majority of task-oriented questions. Their test-retest reliability was generally high, and the non-standard scale was found symmetric and ordinal. CONCLUSION: This questionnaire is relevant for clinical work and EMR systems, provides reliable and interpretable results, and may be used as part of any evaluation effort involving the clinician's perspective of an EMR system. [Abstract/Link to Full Text]

de Lusignan S, Wilson E, Dyble A, Grant T, Theadom A, Chan T
The feasibility of using pattern recognition software to measure the influence of computer use on the consultation.
BMC Med Inform Decis Mak. 2003 Nov 26;312.
BACKGROUND: A key feature of a good general practice consultation is that it is patient-centred. A number of verbal and non-verbal behaviours have been identified as important to establish a good relationship with the patient. However, the use of the computer detracts the doctor's attention away from the patient, compromising these essential elements of the consultation. Current methods to assess the consultation and the influence of the computer on them are time consuming and subjective. If it were possible to measure these quantitatively, it could provide the basis for the first truly objective way of studying the influence of the computer on the consultation.The aim was to assess whether pattern recognition software could be used to measure the influence and pattern of computer use in the consultation. If this proved possible it would provide, for the first time, an objective quantitative measure of computer use and a measure of the attention and responsiveness of the general practitioner towards the patient. METHODS: A feasibility study using pattern recognition software to analyse a consultation was conducted. A web camera, linked to a data-gathering node was used to film a simulated consultation in a standard office. Members of the research team enacted the role of the doctor and the patient, using pattern recognition software to try and capture patient-centred, non-verbal behaviour. As this was a feasibility study detailed results of the analysis are not presented. RESULTS: It was revealed that pattern recognition software could be used to analyse certain aspects of a simulated consultation. For example, trigger lines enabled the number of times the clinician's hand covered the keyboard to be counted and wrapping recorded the number of times the clinician nodded his head. It was also possible to measure time sequences and whether the movement was brief or lingering. CONCLUSION: Pattern recognition software enables movements associated with patient-centredness to be recorded. Pattern recognition software has the potential to provide an objective, quantitative measure of the influence of the computer on the consultation. [Abstract/Link to Full Text]

Colombet I, Dart T, Leneveut L, Zunino S, Ménard J, Chatellier G
A computer decision aid for medical prevention: a pilot qualitative study of the Personalized Estimate of Risks (EsPeR) system.
BMC Med Inform Decis Mak. 2003 Nov 27;313.
BACKGROUND: Many preventable diseases such as ischemic heart diseases and breast cancer prevail at a large scale in the general population. Computerized decision support systems are one of the solutions for improving the quality of prevention strategies. METHODS: The system called EsPeR (Personalized Estimate of Risks) combines calculation of several risks with computerisation of guidelines (cardiovascular prevention, screening for breast cancer, colorectal cancer, uterine cervix cancer, and prostate cancer, diagnosis of depression and suicide risk). We present a qualitative evaluation of its ergonomics, as well as it's understanding and acceptance by a group of general practitioners. We organised four focus groups each including 6-11 general practitioners. Physicians worked on several structured clinical scenarios with the help of EsPeR, and three senior investigators leaded structured discussion sessions. RESULTS: The initial sessions identified several ergonomic flaws of the system that were easily corrected. Both clinical scenarios and discussion sessions identified several problems related to the insufficient comprehension (expression of risks, definition of familial history of disease), and difficulty for the physicians to accept some of the recommendations. CONCLUSION: Educational, socio-professional and organisational components (i.e. time constraints for training and use of the EsPeR system during consultation) as well as acceptance of evidence-based decision-making should be taken into account before launching computerised decision support systems, or their application in randomised trials. [Abstract/Link to Full Text]

Sittig DF
Results of a content analysis of electronic messages (email) sent between patients and their physicians.
BMC Med Inform Decis Mak. 2003 Oct 1;311.
BACKGROUND: Email is the most important mechanism introduced since the telephone for developing interpersonal relationships. This study was designed to provide insight into how patients are using email to request information or services from their healthcare providers. METHODS: Following IRB approval, we reviewed all electronic mail (e-mail) messages sent between five study clinicians and their patients over a one-month period. We used a previously described taxonomy of patient requests to categorize all patient requests contained in the messages. We measured message volume, frequency, length and response time for all messages sent to and received by these clinicians. RESULTS: On average the 5 physicians involved in this study received 40 messages per month, each containing approximately 139 words. Replies sent by the physicians contained 39 words on average and 59.4% of them were sent within 24 hours. Patients averaged 1 request per message. Requests for information on medications or treatments, specific symptoms or diseases, and requests for actions regarding medications or treatments accounted for 75% of all requests. Physicians fulfilled 80.2% of all these requests. Upon comparison of these data to that obtained from traditional office visits, it appears that the potential exists for email encounters to substitute for some percentage of office visits. CONCLUSION: Electronic messaging is an important method for physicians and patients to communicate and further develop their relationship. While many physicians worry that either the number or length of messages from their patients will overwhelm them, there is no evidence to support this. In fact, the evidence suggests that many patient requests, formerly made over the telephone or during office visits, can be addressed via email thus potentially saving both patients and physicians time. [Abstract/Link to Full Text]

Ajuwon GA
Computer and internet use by first year clinical and nursing students in a Nigerian teaching hospital.
BMC Med Inform Decis Mak. 2003 Sep 18;310.
BACKGROUND: The internet is an important source of up-to-date medical information. Although several studies in different countries have explored the extent to which health science students use the computer and the internet, few researches are available on this subject in Nigeria. The aim of this study was to assess the uptake of computer and internet by health science students studying in the country. METHODS: One hundred and eighty three first year medical and nursing students of the University College Hospital, Ibadan, Nigeria, completed a-25 item questionnaire during routine Library Orientation Program in the medical library. The EPI-Info software was used for data analysis. RESULTS: The mean ages for medical students and the student nurses were 22 and 24.6 years respectively. Overall, 42.6% of the entire sample could use the computer, 57.4% could not. While more than half (58%) of the medical students are computer literate, majority (75.9%) of the student nurses are not. Slightly more than two thirds (60.7%) of the entire students had ever used the internet, 33. 9% had not. E-mail was the most popular of internet services used by the students (76.4%) and the cyber café was the common place where students had accessed these services. The students' mean scores on a 15-point perceived self-efficacy scale for internet-related tasks was 3.8 for medical and 0.7 for nursing students (p = 0.00). Students who are computer literate had superior mean scores (4.8) than those without (0.6) (p = 0.000). CONCLUSION: First year clinical and nursing students in Ibadan Nigeria have not fully utilised the opportunity that the use of computer and internet offer for medical education. Improved efforts such as inclusion of computer education in medical and nursing curricular and establishment of computer laboratories are required to increase the student's access to computers and internet. [Abstract/Link to Full Text]

Silva S, Gouveia-Oliveira R, Maretzek A, Carriįo J, Gudnason T, Kristinsson KG, Ekdahl K, Brito-Avô A, Tomasz A, Sanches IS, de Lencastre H, Almeida J
EURISWEB--Web-based epidemiological surveillance of antibiotic-resistant pneumococci in day care centers.
BMC Med Inform Decis Mak. 2003 Jul 8;39.
BACKGROUND: EURIS (European Resistance Intervention Study) was launched as a multinational study in September of 2000 to identify the multitude of complex risk factors that contribute to the high carriage rate of drug resistant Streptococcus pneumoniae strains in children attending Day Care Centers in several European countries. Access to the very large number of data required the development of a web-based infrastructure - EURISWEB - that includes a relational online database, coupled with a query system for data retrieval, and allows integrative storage of demographic, clinical and molecular biology data generated in EURIS. METHODS: All components of the system were developed using open source programming tools: data storage management was supported by PostgreSQL, and the hypertext preprocessor to generate the web pages was implemented using PHP. The query system is based on a software agent running in the background specifically developed for EURIS. RESULTS: The website currently contains data related to 13,500 nasopharyngeal samples and over one million measures taken from 5,250 individual children, as well as over one thousand pre-made and user-made queries aggregated into several reports, approximately. It is presently in use by participating researchers from three countries (Iceland, Portugal and Sweden). CONCLUSION: An operational model centered on a PHP engine builds the interface between the user and the database automatically, allowing an easy maintenance of the system. The query system is also sufficiently adaptable to allow the integration of several advanced data analysis procedures far more demanding than simple queries, eventually including artificial intelligence predictive models. [Abstract/Link to Full Text]

Berman JJ, Henson DE
Classifying the precancers: a metadata approach.
BMC Med Inform Decis Mak. 2003 Jun 20;38.
BACKGROUND: During carcinogenesis, precancers are the morphologically identifiable lesions that precede invasive cancers. In theory, the successful treatment of precancers would result in the eradication of most human cancers. Despite the importance of these lesions, there has been no effort to list and classify all of the precancers. The purpose of this study is to describe the first comprehensive taxonomy and classification of the precancers. As a novel approach to disease classification, terms and classes were annotated with metadata (data that describes the data) so that the classification could be used to link precancer terms to data elements in other biological databases. METHODS: Terms in the UMLS (Unified Medical Language System) related to precancers were extracted. Extracted terms were reviewed and additional terms added. Each precancer was assigned one of six general classes. The entire classification was assembled as an XML (eXtensible Mark-up Language) file. A Perl script converted the XML file into a browser-viewable HTML (HyperText Mark-up Language) file. RESULTS: The classification contained 4700 precancer terms, 568 distinct precancer concepts and six precancer classes: 1) Acquired microscopic precancers; 2) acquired large lesions with microscopic atypia; 3) Precursor lesions occurring with inherited hyperplastic syndromes that progress to cancer; 4) Acquired diffuse hyperplasias and diffuse metaplasias; 5) Currently unclassified entities; and 6) Superclass and modifiers. CONCLUSION: This work represents the first attempt to create a comprehensive listing of the precancers, the first attempt to classify precancers by their biological properties and the first attempt to create a pathologic classification of precancers using standard metadata (XML). The classification is placed in the public domain, and comment is invited by the authors, who are prepared to curate and modify the classification. [Abstract/Link to Full Text]

Gagliardi A, Smith A, Goel V, DePetrillo D
Feasibility study of multidisciplinary oncology rounds by videoconference for surgeons in remote locales.
BMC Med Inform Decis Mak. 2003 Jun 19;37.
BACKGROUND: This study was undertaken to assess the feasibility of using videoconferencing to involve community-based surgeons in interactive, multidisciplinary oncology rounds so they may benefit from the type of community of practice that is usually only available in academic cancer centres. METHODS: An existing videoconference service provider with sites across Ontario was chosen and the series was accredited. Indirect needs assessment involved examining responses to a previously conducted survey of provincial surgeons; interviewing three cancer surgeons from different regions of Ontario; and by analyzing an online portfolio of self-directed learning projects. Direct needs assessment involved a survey of surgeons at videoconference-enabled sites. A surgical, medical and radiation oncologist plus a facilitator were scheduled to guide discussion for each session. A patient scenario developed by the discussants was distributed to participants one week prior to each session. RESULTS: Direct and indirect needs assessment confirmed that breast cancer and colorectal cancer topics were of greatest importance to community surgeons. Six one-hour sessions were offered (two breast, two colorectal, one gynecologic and one lung cancer). A median of 22 physicians and a median of eight sites participated in each session. The majority of respondents were satisfied with the videoconference format, presenters and content. Many noted that discussion prompted reflection on practice and that current practice would change. CONCLUSIONS: This pilot study demonstrated that it is possible to engage remote surgeons in multidisciplinary oncology rounds by videoconference. Continued assessment of videoconferencing is warranted but further research is required to develop frameworks by which to evaluate the benefits of telehealth initiatives. [Abstract/Link to Full Text]

Berman JJ
A tool for sharing annotated research data: the "Category 0" UMLS (Unified Medical Language System) vocabularies.
BMC Med Inform Decis Mak. 2003 Jun 16;36.
BACKGROUND: Large biomedical data sets have become increasingly important resources for medical researchers. Modern biomedical data sets are annotated with standard terms to describe the data and to support data linking between databases. The largest curated listing of biomedical terms is the the National Library of Medicine's Unified Medical Language System (UMLS). The UMLS contains more than 2 million biomedical terms collected from nearly 100 medical vocabularies. Many of the vocabularies contained in the UMLS carry restrictions on their use, making it impossible to share or distribute UMLS-annotated research data. However, a subset of the UMLS vocabularies, designated Category 0 by UMLS, can be used to annotate and share data sets without violating the UMLS License Agreement. METHODS: The UMLS Category 0 vocabularies can be extracted from the parent UMLS metathesaurus using a Perl script supplied with this article. There are 43 Category 0 vocabularies that can be used freely for research purposes without violating the UMLS License Agreement. Among the Category 0 vocabularies are: MESH (Medical Subject Headings), NCBI (National Center for Bioinformatics) Taxonomy and ICD-9-CM (International Classification of Diseases-9-Clinical Modifiers). RESULTS: The extraction file containing all Category 0 terms and concepts is 72,581,138 bytes in length and contains 1,029,161 terms. The UMLS Metathesaurus MRCON file (January, 2003) is 151,048,493 bytes in length and contains 2,146,899 terms. Therefore the Category 0 vocabularies, in aggregate, are about half the size of the UMLS metathesaurus.A large publicly available listing of 567,921 different medical phrases were automatically coded using the full UMLS metatathesaurus and the Category 0 vocabularies. There were 545,321 phrases with one or more matches against UMLS terms while 468,785 phrases had one or more matches against the Category 0 terms. This indicates that when the two vocabularies are evaluated by their fitness to find at least one term for a medical phrase, the Category 0 vocabularies performed 86% as well as the complete UMLS metathesaurus. CONCLUSION: The Category 0 vocabularies of UMLS constitute a large nomenclature that can be used by biomedical researchers to annotate biomedical data. These annotated data sets can be distributed for research purposes without violating the UMLS License Agreement. These vocabularies may be of particular importance for sharing heterogeneous data from diverse biomedical data sets. The software tools to extract the Category 0 vocabularies are freely available Perl scripts entered into the public domain and distributed with this article. [Abstract/Link to Full Text]

Berman JJ, Edgerton ME, Friedman BA
The tissue microarray data exchange specification: a community-based, open source tool for sharing tissue microarray data.
BMC Med Inform Decis Mak. 2003 May 23;35.
BACKGROUND: Tissue Microarrays (TMAs) allow researchers to examine hundreds of small tissue samples on a single glass slide. The information held in a single TMA slide may easily involve Gigabytes of data. To benefit from TMA technology, the scientific community needs an open source TMA data exchange specification that will convey all of the data in a TMA experiment in a format that is understandable to both humans and computers. A data exchange specification for TMAs allows researchers to submit their data to journals and to public data repositories and to share or merge data from different laboratories. In May 2001, the Association of Pathology Informatics (API) hosted the first in a series of four workshops, co-sponsored by the National Cancer Institute, to develop an open, community-supported TMA data exchange specification. METHODS: A draft tissue microarray data exchange specification was developed through workshop meetings. The first workshop confirmed community support for the effort and urged the creation of an open XML-based specification. This was to evolve in steps with approval for each step coming from the stakeholders in the user community during open workshops. By the fourth workshop, held October, 2002, a set of Common Data Elements (CDEs) was established as well as a basic strategy for organizing TMA data in self-describing XML documents. RESULTS: The TMA data exchange specification is a well-formed XML document with four required sections: 1) Header, containing the specification Dublin Core identifiers, 2) Block, describing the paraffin-embedded array of tissues, 3)Slide, describing the glass slides produced from the Block, and 4) Core, containing all data related to the individual tissue samples contained in the array. Eighty CDEs, conforming to the ISO-11179 specification for data elements constitute XML tags used in the TMA data exchange specification. A set of six simple semantic rules describe the complete data exchange specification. Anyone using the data exchange specification can validate their TMA files using a software implementation written in Perl and distributed as a supplemental file with this publication. CONCLUSION: The TMA data exchange specification is now available in a draft form with community-approved Common Data Elements and a community-approved general file format and data structure. The specification can be freely used by the scientific community. Efforts sponsored by the Association for Pathology Informatics to refine the draft TMA data exchange specification are expected to continue for at least two more years. The interested public is invited to participate in these open efforts. Information on future workshops will be posted at http://www.pathologyinformatics.org (API we site). [Abstract/Link to Full Text]

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Recent Articles in Bulletin of the Medical Library Association

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Walton LJ, Hasson S, Ross FV, Martin ER
Outreach to public health professionals: lessons learned from a collaborative Iowa public health project.
Bull Med Libr Assoc. 2000 Apr;88(2):165-71.
In 1995, the National Library of Medicine (NLM) and the Public Health Service (PHS) recommended that special attention be given to the information needs of unaffiliated public health professionals. In response, the National Network of Libraries of Medicine (NN/LM) Greater Midwest Region initiated a collaborative outreach program for public health professionals working in rural east and central Iowa. Five public health agencies were provided equipment, training, and support for accessing the Internet. Key factors in the success of this project were: (1) the role of collaborating agencies in the implementation and ongoing success of information access outreach projects; (2) knowledge of the socio-cultural factors that influence the information-seeking habits of project participants (public health professionals); and (3) management of changing or varying technological infrastructures. Working with their funding, personnel from federal, state, and local governments enhanced the information-seeking skills of public health professionals in rural eastern and central Iowa communities. [Abstract/Link to Full Text]

Gibson KE, Silverberg M
A two-year experience teaching computer literacy to first-year medical students using skill-based cohorts.
Bull Med Libr Assoc. 2000 Apr;88(2):157-64.
Because it is widely accepted that providing information online will play a major role in both the teaching and practice of medicine in the near future, a short formal course of instruction in computer skills was proposed for the incoming class of students entering medical school at the State University of New York at Stony Brook. The syllabus was developed on the basis of a set of expected outcomes, which was accepted by the dean of medicine and the curriculum committee for classes beginning in the fall of 1997. Prior to their arrival, students were asked to complete a self-assessment survey designed to elucidate their initial skill base; the returned surveys showed students to have computer skills ranging from complete novice to that of a systems engineer. The classes were taught during the first three weeks of the semester to groups of students separated on the basis of their knowledge of and comfort with computers. Areas covered included computer basics, e-mail management, MEDLINE, and Internet search tools. Each student received seven hours of hands-on training followed by a test. The syllabus and emphasis of the classes were tailored to the initial skill base but the final test was given at the same level to all students. Student participation, test scores, and course evaluations indicated that this noncredit program was successful in achieving an acceptable level of comfort in using a computer for almost all of the student body. [Abstract/Link to Full Text]

Darmoni SJ, Benichou J, Thirion B, Hellot MF, Fuss J
A study comparing centralized CD-ROM and decentralized intranet access to MEDLINE.
Bull Med Libr Assoc. 2000 Apr;88(2):152-6.
OBJECTIVE: The purpose of this study was to evaluate the efficacy of a decentralized intranet access in each medical department as opposed to centralized unique MEDLINE access in the medical library. DESIGN: A two-phase questionnaire to evaluate MEDLINE use was given to junior and senior physicians at Rouen University Hospital (RUH). Phase I (August-October 1996) corresponded to a time period when centralized access was the only means of access available and phase II (August-October 1997) to a time period following the introduction of decentralized intranet access. RESULTS: A total of 168 physicians filled out at least one phase of the questionnaire, among whom 123 (73%) filled out both phases. Use of MEDLINE significantly increased in 1997 (average of 10.2+/-1.1 searches in three months) versus 1996 (average of 4.9+/-0.7 searches in three months, P<0.0001). The aim of searches changed, becoming significantly more care oriented in phase II (P<0.0001). The number of searches performed by the physicians alone increased (P<0.0001) and searches performed by the librarian decreased (P<0.0001) in phase II. The method of searches also changed, as searches by author (P< 0.0001), by journal (P = 0.0042), and by free word (P = 0.0027) increased in phase II. Knowledge of the following concepts of MEDLINE significantly increased: explosion (P<0.0001), scope note (P<0.0001), Abridged Index Medicus (AIM) journals (P<0.0001), Medical Subject Headings (MeSH) qualifier (P<0.0001), and focus (P<0.0001). CONCLUSION: A decentralized intranet access to MEDLINE increased the number of searches and knowledge of this bibliographic database. MEDLINE intranet access modified the purpose and the methods of searching. [Abstract/Link to Full Text]

Blecic DD
Monograph use at an academic health sciences library: the first three years of shelf life.
Bull Med Libr Assoc. 2000 Apr;88(2):145-51.
OBJECTIVE: To study the circulation of monographs during the first three years of shelf life at an academic health sciences library. METHOD: A record was kept of monographs added to the circulating collection from mid-1994 to mid-1995. After three years, each monograph was located and the number of times it circulated during the first, second, and third year of shelf life determined by counting checkout stamps on the circulation slip. RESULTS: Of the 1,958 monographs studied, 1,674 had complete data for the first three years of shelf life. Of those 1,674 titles, 81.48% circulated at least once. A total of 7,659 circulations were recorded; 38.69% occurred in the first year of shelf life, 32.37% in the second year, and 28.95% in the third year. The data did not fit the well-known 80/20 rule. Instead, approximately 38% of monographs accounted for 80% of circulation. A small percentage, 2.21%, of monographs accounted for a substantial percentage of circulation, 21.84%. CONCLUSIONS: A large percentage of the monographs circulated and use did not decline sharply with age within the first three years of shelf life, indicating a high demand for monographs at this academic health sciences library. These results, combined with the findings of earlier studies, suggested two possibilities. First, academic health sciences libraries might exhibit use of a higher percentage of monograph acquisitions than other types of libraries; or, second, a low monograph-to-user ratio might result in a higher percentage of monographs being used. Perhaps both factors contributed to the results found in this study. Further investigation would be needed to determine the extent to which library type and monograph-to-user ratio influenced monograph use. [Abstract/Link to Full Text]

Sable JH, Carlin BG, Andrews JE, Sievert MC
Creating local bibliographic databases: new tools for evidence-based health care.
Bull Med Libr Assoc. 2000 Apr;88(2):139-44.
The Internet has created new opportunities for librarians to present literature search results to clinicians. In order to take full advantage of these opportunities, libraries need to create locally maintained bibliographic databases. A simple method of creating a local bibliographic database and publishing it on the Web is described. The method uses off-the-shelf software and requires minimal programming. A hedge search strategy for outcome studies of clinical process interventions is created, and Ovid is used to search MEDLINE. The search results are saved and imported into EndNote libraries. The citations are modified, exported to a Microsoft Access database, and published on the Web. Clinicians can use a Web browser to search the database. The bibliographic database contains 13,803 MEDLINE citations of outcome studies. Most searches take between four and ten seconds and retrieve between ten and 100 citations. The entire cost of the software is under $900. Locally maintained bibliographic databases can be created easily and inexpensively. They significantly extend the evidence-based health care services that libraries can offer to clinicians. [Abstract/Link to Full Text]

Homan JM
A snapshot in time: citation rankings of the Bulletin of the Medical Library Association.
Bull Med Libr Assoc. 2000 Jan;88(1):83. [Abstract/Link to Full Text]

Johnson ME
Electronic current awareness for mental health facilities.
Bull Med Libr Assoc. 2000 Jan;88(1):77-80. [Abstract/Link to Full Text]

Blecic DD, Robinson AE
Use of print journals in an intracampus exchange program: implications for service and electronic journal subscriptions.
Bull Med Libr Assoc. 2000 Jan;88(1):75-7. [Abstract/Link to Full Text]

Huber JT, Swigger K
Preparing health information professionals for the twenty-first century: the Texas Woman's University dual master's degree program.
Bull Med Libr Assoc. 2000 Jan;88(1):72-4. [Abstract/Link to Full Text]

Dimitroff A
Electronic access in Russian medical libraries.
Bull Med Libr Assoc. 2000 Jan;88(1):70-2. [Abstract/Link to Full Text]

Hollander SM
Providing health information to the general public: a survey of current practices in academic health sciences libraries.
Bull Med Libr Assoc. 2000 Jan;88(1):62-9.
A questionnaire was mailed to 148 publicly and privately supported academic health sciences libraries affiliated with Association of American Medical Colleges (AAMC-accredited medical schools in the United States and Canada to determine level of access and services provided to the general public. For purposes of this study, "general public" was defined as nonaffiliated students or health care professionals, attorneys and other nonhealth-related professionals, patients from affiliated or other hospitals or clinics, and general consumers. One hundred five (71%) libraries responded. Results showed 98% of publicly supported libraries and 88% of privately supported libraries provided access to some or all of the general public. Publicly supported libraries saw greater numbers of public patrons, often provided more services, and were more likely to circulate materials from their collections than were privately supported libraries. A significant number of academic health sciences libraries housed a collection of consumer-oriented materials and many provided some level of document delivery service, usually for a fee. Most allowed the public to use some or all library computers. Results of this study indicated that academic health sciences libraries played a significant role in serving the information-seeking public and suggested a need to develop written policies or guidelines covering the services that will be provided to minimize the impact of this service on primary clientele. [Abstract/Link to Full Text]

Macias-Chapula CA
AIDS in Haiti: a bibliometric analysis.
Bull Med Libr Assoc. 2000 Jan;88(1):56-61.
OBJECTIVES: In Haiti, AIDS has become the leading cause of death in sexually active adults. Increasingly, AIDS has become a disease of women and children. Previous bibliometric studies have shown the emergence of Haiti as a leading country in the production of AIDS literature in the Latin American and Caribbean regions. No information exists, however, regarding the type of publications produced, the collaboration patterns used, or the subject content analysis of this production. The purpose of this study was to gain insight into the construction of this literature production. METHODS: A bibliometric analysis regarding Haitian AIDS research was conducted in the AIDSLINE database for the period 1980 to 1998. An attempt was made to identify the patterns of the growth in AIDS literature, as well as the types of documents published, authorship, institutional affiliations of authors, and subject content. RESULTS: Results indicated that most documents were published in periodicals. The International Conference on AIDS obtained the highest frequency. The United States, Haiti, and Canada were the main productive countries. CONCLUSIONS: While nearly 40% of the records corresponded to ethnology-related articles, HIV infections, sex behavior, pregnancy, and substance-related disorders headed the Medical Subject Headings (MeSH) found. Main aspects of AIDS papers focused on epidemiology, complications, and trends issues. [Abstract/Link to Full Text]

Smith RD, Williams M
Applications of informatics in veterinary medicine.
Bull Med Libr Assoc. 2000 Jan;88(1):49-55.
This study used the peer-reviewed biomedical literature to define the veterinary informatics knowledgebase and associated subspecialties, and assesses the level of activity in the field over the thirty-year period from 1966 through 1995. Grateful Med was used to search the MEDLINE bibliographic database for articles that shared one or more Medical Subject Headings (MeSH) keywords from the veterinary and medical informatics subject headings. Each of ninety-five MeSH medical informatics terms was assigned to one of twelve veterinary informatics subspecialties. The number of articles retrieved by each MeSH keyword and subspecialty was calculated. A total of 611 articles were retrieved, representing the contributions of 1,338 authors published in 153 journals. The field experienced slow growth over the twenty-year period from 1966 through 1985. In the following decade, the cumulative number of veterinary informatics articles almost tripled and the percentage of veterinary-related articles that included an informatics component increased almost two-and-one-half fold. Despite this recent growth, the number of veterinary-related articles with an informatics component has never exceeded 1% of either the veterinary or medical informatics literature over the past thirty years, and representation of veterinary subspecialties in the literature varied widely. [Abstract/Link to Full Text]

Yarfitz S, Ketchell DS
A library-based bioinformatics services program.
Bull Med Libr Assoc. 2000 Jan;88(1):36-48.
Support for molecular biology researchers has been limited to traditional library resources and services in most academic health sciences libraries. The University of Washington Health Sciences Libraries have been providing specialized services to this user community since 1995. The library recruited a Ph.D. biologist to assess the molecular biological information needs of researchers and design strategies to enhance library resources and services. A survey of laboratory research groups identified areas of greatest need and led to the development of a three-pronged program: consultation, education, and resource development. Outcomes of this program include bioinformatics consultation services, library-based and graduate level courses, networking of sequence analysis tools, and a biological research Web site. Bioinformatics clients are drawn from diverse departments and include clinical researchers in need of tools that are not readily available outside of basic sciences laboratories. Evaluation and usage statistics indicate that researchers, regardless of departmental affiliation or position, require support to access molecular biology and genetics resources. Centralizing such services in the library is a natural synergy of interests and enhances the provision of traditional library resources. Successful implementation of a library-based bioinformatics program requires both subject-specific and library and information technology expertise. [Abstract/Link to Full Text]

Atlas MC
The rise and fall of the medical mediated searcher.
Bull Med Libr Assoc. 2000 Jan;88(1):26-35.
The relationship between the development of mediated online literature searching and the recruitment of medical librarians to fill positions as online searchers was investigated. The history of database searching by medical librarians was outlined and a content analysis of thirty-five years of job advertisements in MLA News from 1961 through 1996 was summarized. Advertisements for online searchers were examined to test the hypothesis that the growth of mediated online searching was reflected in the recruitment of librarians to fill positions as mediated online searchers in medical libraries. The advent of end-user searching was also traced to determine how this trend affected the demand for mediated online searching and job availability of online searchers. Job advertisements were analyzed to determine what skills were in demand as end-user searching replaced mediated online searching as the norm in medical libraries. Finally, the trend away from mediated online searching to support of other library services was placed in the context of new roles for medical librarians. [Abstract/Link to Full Text]

Graves KJ
Electronic reserves: copyright and permissions.
Bull Med Libr Assoc. 2000 Jan;88(1):18-25.
Electronic reserves present a new service option for libraries to provide needed materials during hours that the library is not open and to user groups located some distance from library collections. Possible changes to current copyright law and publishers permissions policies have delayed the development of electronic reserves in many libraries. This paper reviews the current state of electronic reserves materials in the publishing and library communities and presents the results of a survey of publishers to determine permissions policies for electronic materials. Issues of concern to both libraries and publishers are discussed. [Abstract/Link to Full Text]

Miller N, Lacroix EM, Backus JE
MEDLINEplus: building and maintaining the National Library of Medicine's consumer health Web service.
Bull Med Libr Assoc. 2000 Jan;88(1):11-7.
MEDLINEplus is a Web-based consumer health information resource, made available by the National Library of Medicine (NLM). MEDLINEplus has been designed to provide consumers with a well-organized, selective Web site facilitating access to reliable full-text health information. In addition to full-text resources, MEDLINEplus directs consumers to dictionaries, organizations, directories, libraries, and clearinghouses for answers to health questions. For each health topic, MEDLINEplus includes a preformulated MEDLINE search created by librarians. The site has been designed to match consumer language to medical terminology. NLM has used advances in database and Web technologies to build and maintain MEDLINEplus, allowing health sciences librarians to contribute remotely to the resource. This article describes the development and implementation of MEDLINEplus, its supporting technology, and plans for future development. [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]

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

Walter G
"Rubber stamping" retracted papers.
Bull Med Libr Assoc. 2000 Jan;88(1):85. [Abstract/Link to Full Text]

Budd JM, Sievert M, Schultz TR, Scoville C
Effects of article retraction on citation and practice in medicine.
Bull Med Libr Assoc. 1999 Oct;87(4):437-43.
At times, there are reasons for authors to make a formal statement of retraction of work they publish in biomedical journals. This study examines 235 retracted articles and looks at the reasons for these retractions and citations to the articles subsequent to retraction. The primary reasons for retraction are error of various kinds (such as problems with method or sample, including contamination of samples) and misconduct. The 235 articles are cited a total of 2,034 times after retraction. This set of citations can be divided into two groups: citations that appear in journals included in the Abridged Index Medicus and those that appear in other journals included in MEDLINE. While most of the citations in these two groups of journals can be categorized as "implicitly positive," 275 make explicitly positive mention of retracted articles. The implications for continued citation for biomedical research and clinical practice are discussed. [Abstract/Link to Full Text]

Viera A
Marking retracted papers at The Webster Pendergrass Agriculture Veterinary Medicine Library.
Bull Med Libr Assoc. 2000 Jul;88(3):273. [Abstract/Link to Full Text]

Homan JM
E-biomed.
Bull Med Libr Assoc. 1999 Oct;87(4):485-6. [Abstract/Link to Full Text]

Thirion B, Darmoni SJ
Simplified access to MeSH tree structures on CISMeF.
Bull Med Libr Assoc. 1999 Oct;87(4):480-1. [Abstract/Link to Full Text]

Foust JE, Tannery NH, Detlefsen EG
Implementation of a Web-based tutorial.
Bull Med Libr Assoc. 1999 Oct;87(4):477-9. [Abstract/Link to Full Text]

Burrows SC, Tylman V
Evaluating medical student searches of MEDLINE for evidence-based information: process and application of results.
Bull Med Libr Assoc. 1999 Oct;87(4):471-6.
OBJECTIVE: To evaluate the adequacy of the MEDLINE instruction routinely given to all entering medical students at the University of Miami School of Medicine and the ability of students to search effectively for and retrieve evidence-based information for clinical decision making by the end of their third-year. METHODOLOGY: The authors developed and implemented a strategy for evaluating the search strategies and articles selected by third-year students, who participated in the Objective Structured Clinical Examination (OSCE) in June 1996, 1997, and 1998, and reviewed the literature on evidence-based medicine and evaluation of medical student searches. RESULTS: A mean of 5% of the students' search strategies and a mean of 26% of articles selected were ranked "excellent" or "good"; a mean of 26% of search strategies were ranked "fair" and a mean of 69% were ranked "poor"; and a mean of 22% of articles selected were ranked "fair" and a mean of 52% were ranked "poor" based on the strategy developed to evaluate student searches. CONCLUSIONS: Evaluating medical student searches for evidence-based information is an effective way of evaluating students' searching proficiency, and, in turn, the adequacy of the instruction they receive. Based on the results of the OSCE test, the school of medicine expanded the library's educational role and the library implemented major changes in the training program. Information on evidence-based medicine is now incorporated into the MEDLINE instruction. Library faculty evaluate the required searches performed by students for evidence-based information during their first and second years; 30% of students are identified for follow-up, individualized instruction based on the evaluation; and a new case-based curriculum has been proposed with a fourteen-week problem-based learning (PBL) block. These developments are timely in light of the evidence-based competencies recently published by the Association of American Medical Colleges. [Abstract/Link to Full Text]

McGowan JJ, Winstead-Fry P
Problem Knowledge Couplers: reengineering evidence-based medicine through interdisciplinary development, decision support, and research.
Bull Med Libr Assoc. 1999 Oct;87(4):462-70.
The rapid growth of medical knowledge is creating a demand for new ways of providing information in support of evidence-based medical practice. Problem Knowledge Couplers are a clinical decision support software tool that offer a new approach to this growing problem. Couplers are developed through a collaboration among clinicians, informaticians, and librarians. They recognize that functionality must be predicated upon combining unique patient information, gleaned through relevant structured question sets, with the appropriate knowledge found in the world's peer-reviewed medical literature. Two pilot studies indicate that couplers can meet the gold standards of decision making within both a primary care and a specialty practice. Issues remain about how to best integrate Problem Knowledge Couplers into clinical practice and whether large-scale outcomes research will support the findings of pilot studies. However, Problem Knowledge Couplers represent a promising approach that might portend a new model for health care delivery in the next millennium. [Abstract/Link to Full Text]

Wu G, Li J
Comparing Web search engine performance in searching consumer health information: evaluation and recommendations.
Bull Med Libr Assoc. 1999 Oct;87(4):456-61.
Identifying and accessing reliable, relevant consumer health information rapidly on the Internet may challenge the health sciences librarian and layperson alike. In this study, seven search engines are compared using representative consumer health topics for their content relevancy, system features, and attributes. The paper discusses evaluation criteria; systematically compares relevant results; analyzes performance in terms of the strengths and weaknesses of the search engines; and illustrates effective search engine selection, search formulation, and strategies. [Abstract/Link to Full Text]

Mouillet E
Language barriers and bibliographic retrieval effectiveness: use of MEDLINE by French-speaking end users.
Bull Med Libr Assoc. 1999 Oct;87(4):451-5.
OBJECTIVE: A study was conducted to determine if bibliographic retrieval performed by French-speaking end users is impaired by English language interfaces. The American database MEDLINE on CD-ROM was used as a model. METHODS: A survey of self-administered questionnaires was performed at two libraries of Victor Segalen Bordeaux 2 University, during a two-month period in 1997. Three study groups were constituted: MEDLINE / Ovid end users, MEDLINE / Ovid librarian-mediated users, and Pascal, a French bibliographic database, end users. RESULTS: Among 191 respondents, only 22% thought English was an obstacle to their bibliographic retrieval. However, the research software was generally underused and the quality of the retrieval weak. The differences were statistically significant between users trained by librarians and the self-trained group, the former performing better. CONCLUSION: Special efforts need to be made to develop curriculum training programs for computerized bibliographic retrieval in medical schools, regardless of the native language of the student. [Abstract/Link to Full Text]

Baker LM, Pettigrew KE
Theories for practitioners: two frameworks for studying consumer health information-seeking behavior.
Bull Med Libr Assoc. 1999 Oct;87(4):444-50.
Consumer health information studies in library and information science (LIS) are typically not grounded within a theoretical framework. This article explains the importance of theory to LIS research in general, and the specific value of using theories from other disciplines to study consumers' health information-seeking behavior. The argument is supported with two examples: Miller's psychological theory of blunting and monitoring behavior and Granovetter's sociological theory of the strength of weak ties. These theories can be applied by practitioner-researchers to investigate a variety of research problems. [Abstract/Link to Full Text]

Bowden VM
Health sciences library building projects, 1998 survey.
Bull Med Libr Assoc. 1999 Oct;87(4):415-36.
Twenty-eight health sciences library building projects are briefly described, including twelve new buildings and sixteen additions, remodelings, and renovations. The libraries range in size from 2,144 square feet to 190,000 gross square feet. Twelve libraries are described in detail. These include three hospital libraries, one information center sponsored by ten institutions, and eight academic health sciences libraries. [Abstract/Link to Full Text]

Lynch C
Medical libraries, bioinformatics, and networked information: a coming convergence?
Bull Med Libr Assoc. 1999 Oct;87(4):408-14.
Libraries will be changed by technological and social developments that are fueled by information technology, bioinformatics, and networked information. Libraries in highly focused settings such as the health sciences are at a pivotal point in their development as the synthesis of historically diverse and independent information sources transforms health care institutions. Boundaries are breaking down between published literature and research data, between research databases and clinical patient data, and between consumer health information and professional literature. This paper focuses on the dynamics that are occurring with networked information sources and the roles that libraries will need to play in the world of medical informatics in the early twenty-first century. [Abstract/Link to Full Text]

Holtum EA
Librarians, clinicians, evidence-based medicine, and the division of labor.
Bull Med Libr Assoc. 1999 Oct;87(4):404-7.
Have librarians promoted end user searching to the detriment of the profession and promoted clinical inefficiency from causally trained health practitioners? Issues related to the complexity of bibliographic retrieval in the networked environment are explored within the context of evidence-based medicine and the division of labor. [Abstract/Link to Full Text]

Fuller SS, Ketchell DS, Tarczy-Hornoch P, Masuda D
Integrating knowledge resources at the point of care: opportunities for librarians.
Bull Med Libr Assoc. 1999 Oct;87(4):393-403.
Health sciences librarians at the University of Washington (UW) are partners in the evolution of Internet-based clinical information systems for two medical centers, University of Washington Medical Center and Harborview Medical Center, as well as the UW Primary Care Network clinics. Librarians lead information resource and systems development projects and play a variety of roles including facilitator, publisher, integrator, and educator. These efforts have been coordinated with parallel development efforts by the Integrated Advanced Information Management Systems (IAIMS) clinical informatics group in developing electronic medical record systems and clinical decision support tools. The outcome is MINDscape, a very heavily used Web view of the patient medical record with tightly integrated knowledge resources as well as numerous Web-accessible information resources and tools. The goal of this article is to provide a case study of librarian involvement in institutional information systems development at UW and to illustrate the variety of roles that librarians can assume in hospital settings. [Abstract/Link to Full Text]

McGrath F, Morgenweck L
Rebuilding a clinical workstation with spider's silk of the Web.
Bull Med Libr Assoc. 1999 Oct;87(4):387-92.
The Yale-New Haven Hospital (YNHH) clinical workstation came into existence in 1993 to provide a simple menu-driven interface to high use information systems that would be easily accessible on the wards and in the intensive care units. Direct Internet access, advances in Web-based software, and greater cooperation between Yale-New Haven Hospital and Yale School of Medicine network technology groups have enabled the clinical workstations to become an integral tool for providing clinical care. The workstation provides bedside access to an expanding array of internal and external resources to support patient care and has the potential to become the basis for an interface that will be utilized throughout the multi-location Yale-New Haven Healthcare System. [Abstract/Link to Full Text]

Doyle JD
IAIMS and JCAHO: implications for hospital librarians. Integrated Academic Information Management Systems. Joint Commission on Accreditation of Healthcare Organizations.
Bull Med Libr Assoc. 1999 Oct;87(4):383-6.
The roles of hospital librarians have evolved from keeping print materials to serving as a focal point for information services and structures within the hospital. Concepts that emerged from the Integrated Academic Information Management Systems (IAIMS) as described in the Matheson Report and the 1994 Joint Commission on Accreditation of Healthcare Organizations (JCAHO) standards have combined to propel hospital libraries into many new roles and functions. This paper will review the relationship of the two frameworks, provide a view of their commonalities, and establish the advantages of both for hospital librarianship as a profession. [Abstract/Link to Full Text]

Zenan JS
Frieda O. Weise, Medical Library Association President 1999-2000.
Bull Med Libr Assoc. 1999 Jul;87(3):357-60. [Abstract/Link to Full Text]

Homan JM
Pecksniffs at the AMA?
Bull Med Libr Assoc. 1999 Jul;87(3):351-2. [Abstract/Link to Full Text]

Ash JS, Hersh WR, Krages KP, Morgan JE, Schumacher R
The Oregon IAIMS: then and now.
Bull Med Libr Assoc. 1999 Jul;87(3):347-9. [Abstract/Link to Full Text]

Yue W, Pittman S, Wilson CS
Selection of useful links for an Australian Medical Association Web site.
Bull Med Libr Assoc. 1999 Jul;87(3):343-6. [Abstract/Link to Full Text]

Groen F
Fin-de-sičcle Philadelphia and the founding of the Medical Library Association.
Bull Med Libr Assoc. 1999 Jul;87(3):337-42.
Philadelphia at the time of the founding of the Medical Library Association (MLA) is described. Several factors that promoted the birth of the association are discussed, including the rapid increase in the labor force and the rise of other health related professions, such as the American Hospital Association and the professionalization of nursing. The growth of the public hygiene movement in Philadelphia at the time of Sir William Osler's residency in the city is discussed. Finally, the rapid growth of the medical literature is considered a factor promoting the development of the association. This article continues the historical consideration of the MLA begun in the author's article on the three founders of the association. The background information is drawn from the items listed in the bibliography, and the conclusions are those of the author. [Abstract/Link to Full Text]

Hollander SM, Martin ER
Public health professionals in the Midwest: a profile of connectivity and information technology skills.
Bull Med Libr Assoc. 1999 Jul;87(3):329-36.
OBJECTIVES: The aim of this study was to assess Internet connections and information technology skills of public health workers in the Midwest. METHODS: A questionnaire was mailed to 713 local health departments (LHDs) in the ten states of the Greater Midwest Region. RESULTS: Three hundred forty-four LHDs (48%) responded. Overall, 85% own a computer that would allow Internet access. Half provide Internet access to some or all staff. Of these, two-thirds use e-mail and half search the Web. One-half are linked to the State Health Department, and 30% are linked to other local health departments. Over half use CDC-Wonder; less than 20% search MEDLINE. Two-thirds of the respondents expressed an interest in MEDLINE training, and three-fourths are interested in learning more about the Internet. Sixty-nine percent of respondents planned to enhance electronic communication capacity within the next year. CONCLUSIONS: Public health practitioners need timely, convenient access to information to aid them in improving the health of the American public. A majority of public health departments in the Midwest are technically capable of connecting to the Internet. This technological capability, combined with an expressed desire by public health agencies to have workers become computer literate, suggests an important role for health sciences librarians. [Abstract/Link to Full Text]

Scherrer CS, Dorsch JL
The evolving role of the librarian in evidence-based medicine.
Bull Med Libr Assoc. 1999 Jul;87(3):322-8.
Librarians' participation in evidence-based medicine (EBM) is rooted in past practices, most notably in clinical medical librarianship. EBM extends the librarians' role beyond identification of the literature to involvement in practicing and teaching quality filtering and critical appraisal of the literature. These activities require librarians to acquire new knowledge and develop new skills. A professional development program for librarians at the Library of the Health Sciences (LHS) at the University of Illinois at Chicago (UIC) is described. The program's goals are to increase librarians' skills and support the EBM curricular initiative at the UIC College of Medicine (COM). The unique program has been a collaborative effort of the LHS and the COM. The locally developed classes provide librarians with instruction in clinical study designs, statistical concepts, and critical appraisal of the literature. Other interventions such as an EBM round table are also described. The programs' success is measured by librarians' growing involvement in EBM medical curricula, journal clubs, and morning reports. Additionally, librarians gained competence in new skills and professional satisfaction from working collegially with COM students, residents, and faculty. [Abstract/Link to Full Text]

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Recent Articles in Journal of the American Medical Informatics Association

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Holzmueller CG, Pronovost PJ, Dickman F, Thompson DA, Wu AW, Lubomski LH, Fahey M, Steinwachs DM, Engineer L, Jaffrey A, Morlock LL, Dorman T
Creating the web-based intensive care unit safety reporting system.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):130-9.
In an effort to improve patient safety, researchers at the Johns Hopkins University designed and implemented a comprehensive Web-based Intensive Care Unit Safety Reporting System (ICUSRS). The ICUSRS collects data about adverse events and near misses from all staff in the ICU. This report reflects data on 854 reports from 18 diverse ICUs across the United States. Reporting is voluntary, and data collected is confidential, with patient, provider, and reporter information deidentified. Preliminary data include system factors reported, degree of patient harm, reporting times, and evaluations of the system. Qualitative and quantitative data are reported back to the ICU site study teams and frontline staff through monthly reports, case discussions, and a quarterly newsletter. [Abstract/Link to Full Text]

Frassica JJ
Frequency of laboratory test utilization in the intensive care unit and its implications for large-scale data collection efforts.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):229-33.
OBJECTIVE: Mapping local use names to standardized nomenclatures such as LOINC (Logical Observation Identifiers Names and Codes) is a time-consuming task when done retrospectively or during the configuration of new information systems. The author sought to identify a subset of intensive care unit (ICU) laboratory tests, which, because of their frequency of use, should be the focus of efforts to standardize test names in ICU information systems. DESIGN: The author reviewed the ordering practices in medical, surgical, and pediatric ICUs within a large university teaching hospital to identify the subset of laboratory tests that represented the majority of tests performed in these settings. The author compared the results of his findings with the laboratory tests required to complete several of the most frequently used ICU acuity scoring systems. RESULTS: It was found that between 104 and 202 tests and profiles represented 99% of all testing in the three ICUs. All the laboratory studies needed for six commonly used ICU scoring systems fell into the top 21 laboratory studies and profiles performed in each ICU. CONCLUSION: The author identified a small subset of the LOINC database that should be the focus of efforts to standardize test names in ICU information systems. Mapping this subset of laboratory tests and profiles to LOINC vocabulary will simplify the process of collecting data for large-scale databases such as ICU scoring systems and the configuration of new ICU information systems. [Abstract/Link to Full Text]

Ely JW, Osheroff JA, Chambliss ML, Ebell MH, Rosenbaum ME
Answering physicians' clinical questions: obstacles and potential solutions.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):217-24.
OBJECTIVE: To identify the most frequent obstacles preventing physicians from answering their patient-care questions and the most requested improvements to clinical information resources. DESIGN: Qualitative analysis of questions asked by 48 randomly selected generalist physicians during ambulatory care. MEASUREMENTS: Frequency of reported obstacles to answering patient-care questions and recommendations from physicians for improving clinical information resources. RESULTS: The physicians asked 1,062 questions but pursued answers to only 585 (55%). The most commonly reported obstacle to the pursuit of an answer was the physician's doubt that an answer existed (52 questions, 11%). Among pursued questions, the most common obstacle was the failure of the selected resource to provide an answer (153 questions, 26%). During audiotaped interviews, physicians made 80 recommendations for improving clinical information resources. For example, they requested comprehensive resources that answer questions likely to occur in practice with emphasis on treatment and bottom-line advice. They asked for help in locating information quickly by using lists, tables, bolded subheadings, and algorithms and by avoiding lengthy, uninterrupted prose. CONCLUSION: Physicians do not seek answers to many of their questions, often suspecting a lack of usable information. When they do seek answers, they often cannot find the information they need. Clinical resource developers could use the recommendations made by practicing physicians to provide resources that are more useful for answering clinical questions. [Abstract/Link to Full Text]

Peleg M, Rubin D, Altman RB
Using Petri Net tools to study properties and dynamics of biological systems.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):181-99.
Petri Nets (PNs) and their extensions are promising methods for modeling and simulating biological systems. We surveyed PN formalisms and tools and compared them based on their mathematical capabilities as well as by their appropriateness to represent typical biological processes. We measured the ability of these tools to model specific features of biological systems and answer a set of biological questions that we defined. We found that different tools are required to provide all capabilities that we assessed. We created software to translate a generic PN model into most of the formalisms and tools discussed. We have also made available three models and suggest that a library of such models would catalyze progress in qualitative modeling via PNs. Development and wide adoption of common formats would enable researchers to share models and use different tools to analyze them without the need to convert to proprietary formats. [Abstract/Link to Full Text]

Rubin DL, Thorn CF, Klein TE, Altman RB
A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):121-9.
OBJECTIVE: Biomedical databases summarize current scientific knowledge, but they generally require years of laborious curation effort to build, focusing on identifying pertinent literature and data in the voluminous biomedical literature. It is difficult to manually extract useful information embedded in the large volumes of literature, and automated intelligent text analysis tools are becoming increasingly essential to assist in these curation activities. The goal of the authors was to develop an automated method to identify articles in Medline citations that contain pharmacogenetics data pertaining to gene-drug relationships. DESIGN: The authors built and evaluated several candidate statistical models that characterize pharmacogenetics articles in terms of word usage and the profile of Medical Subject Headings (MeSH) used in those articles. The best-performing model was used to scan the entire Medline article database (11 million articles) to identify candidate pharmacogenetics articles. RESULTS: A sampling of the articles identified from scanning Medline was reviewed by a pharmacologist to assess the precision of the method. The authors' approach identified 4,892 pharmacogenetics articles in the literature with 92% precision. Their automated method took a fraction of the time to acquire these articles compared with the time expected to be taken to accumulate them manually. The authors have built a Web resource (http://pharmdemo.stanford.edu/pharmdb/main.spy) to provide access to their results. CONCLUSION: A statistical classification approach can screen the primary literature to pharmacogenetics articles with high precision. Such methods may assist curators in acquiring pertinent literature in building biomedical databases. [Abstract/Link to Full Text]

Aphinyanaphongs Y, Tsamardinos I, Statnikov A, Hardin D, Aliferis CF
Text categorization models for high-quality article retrieval in internal medicine.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):207-16.
OBJECTIVE Finding the best scientific evidence that applies to a patient problem is becoming exceedingly difficult due to the exponential growth of medical publications. The objective of this study was to apply machine learning techniques to automatically identify high-quality, content-specific articles for one time period in internal medicine and compare their performance with previous Boolean-based PubMed clinical query filters of Haynes et al. DESIGN The selection criteria of the ACP Journal Club for articles in internal medicine were the basis for identifying high-quality articles in the areas of etiology, prognosis, diagnosis, and treatment. Naive Bayes, a specialized AdaBoost algorithm, and linear and polynomial support vector machines were applied to identify these articles. MEASUREMENTS The machine learning models were compared in each category with each other and with the clinical query filters using area under the receiver operating characteristic curves, 11-point average recall precision, and a sensitivity/specificity match method. RESULTS In most categories, the data-induced models have better or comparable sensitivity, specificity, and precision than the clinical query filters. The polynomial support vector machine models perform the best among all learning methods in ranking the articles as evaluated by area under the receiver operating curve and 11-point average recall precision. CONCLUSION This research shows that, using machine learning methods, it is possible to automatically build models for retrieving high-quality, content-specific articles using inclusion or citation by the ACP Journal Club as a gold standard in a given time period in internal medicine that perform better than the 1994 PubMed clinical query filters. [Abstract/Link to Full Text]

Forster AJ, Andrade J, van Walraven C
Validation of a discharge summary term search method to detect adverse events.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):200-6.
OBJECTIVE: Adverse events are poor health outcomes caused by medical care. Measuring them is necessary for quality improvements, but current detection methods are inadequate. We performed this study to validate a previously derived method of adverse event detection using term searching in physician-dictated discharge summaries. DESIGN: This was a retrospective, chart review study of a random sample of 245 adult medicine and surgery patients admitted to a multicampus academic medical center in 2002. MEASUREMENTS: The authors used a commercially available search engine to scan discharge summaries for the presence of 104 terms that potentially indicate an adverse event. Summaries with any of these terms were reviewed by a physician to determine the term's context. Screen-positive summaries had a term that was contextually indicative of an adverse event. We used a two-stage chart review as the gold standard to determine the true presence or absence of an adverse event. RESULTS: The average patient age was 62 years (standard deviation 18.6) and 55% were admitted to a medical service. By gold standard criteria, 48 of 245 patients had an adverse event. Term searching classified 27 cases with an adverse event, with 11 true positives; 218 cases were classified as not having an adverse event, with 181 true negatives. The sensitivity, specificity, and positive and negative predictive values were 0.23 (95% confidence interval [CI]=0.11-0.35), 0.92 (95% CI=0.88-0.96), 0.41 (95% CI=0.25-0.59), and 0.83 (95% CI=95% 0.77-0.97), respectively. CONCLUSION: Although the sensitivity of the method is low, its high specificity means that the method could be used to replace expensive manual chart reviews by nurses. [Abstract/Link to Full Text]

Poliakov AV, Albright E, Hinshaw KP, Corina DP, Ojemann G, Martin RF, Brinkley JF
Server-based approach to web visualization of integrated three-dimensional brain imaging data.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):140-51.
The authors describe a client-server approach to three-dimensional (3-D) visualization of neuroimaging data, which enables researchers to visualize, manipulate, and analyze large brain imaging datasets over the Internet. All computationally intensive tasks are done by a graphics server that loads and processes image volumes and 3-D models, renders 3-D scenes, and sends the renderings back to the client. The authors discuss the system architecture and implementation and give several examples of client applications that allow visualization and analysis of integrated language map data from single and multiple patients. [Abstract/Link to Full Text]

Hsu J, Huang J, Kinsman J, Fireman B, Miller R, Selby J, Ortiz E
Use of e-Health services between 1999 and 2002: a growing digital divide.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):164-71.
OBJECTIVE: To evaluate the patterns of e-Health use over a four-year period and the characteristics of users. DESIGN: Longitudinal, population-based study (1999-2002) of members of a prepaid integrated delivery system. Available e-Health services included ordering prescription drug refills, scheduling appointments, and asking medical questions. MEASUREMENTS: Rates of known access to e-Health services, and of e-Health use each quarter. RESULTS: The number of members with known e-Health access increased from 51,336 (1.6%) in 1999 to 324,522 (9.3%), in 2002. The percentage of households in which at least one person in the household had access increased from 2.7% to 14.1%. Among the subjects with known access, the percentage of subjects that used e-Health at least once increased from 25.7% in 1999 to 36.2% in 2002. In the multivariate analysis, subjects who had a low expected clinical need, were nonwhite, or lived in low socioeconomic status (SES) neighborhoods were less likely to have used e-Health services in 2002. Disparities by race/ethnicity and SES persisted after controlling for access to e-Health and widened over time. CONCLUSION: Access to and use of e-Health services are growing rapidly. Use of these services appears to be greatest among persons with more medical need. The majority of subjects, however, do not use any e-Health services. More research is needed to determine potential reasons for disparities in e-Health use by race/ethnicity and SES as well as the implications of these disparities on clinical outcomes. [Abstract/Link to Full Text]

Overhage JM, Evans L, Marchibroda J
Communities' readiness for health information exchange: the National Landscape in 2004.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):107-12.
BACKGROUND: The Secretary of Health and Human Services recently released a report calling for the nation to create a national health information network (NHIN) that would interconnect Regional Health Information Organizations (RHIOs). These RHIOs, which others have called Local or Regional Health Information Infrastructures (LHII), would in turn interconnect local as well as national health information resources. Little data exist about the activities taking place in communities to create LHIIs. APPROACH: The authors analyzed data that communities submitted in response to a request for capabilities issued by the Foundation for eHealth as part of their Connecting Communities for Better Health program using descriptive statistics and subjective evaluation. IMPRESSION: The authors analyzed data from 134 responses from communities in 42 states and the District of Columbia. Communities are enthusiastic about moving forward with health information exchange to create LHIIs to improve the efficiency, quality, and safety of care. They have identified significant local sources of investment and plan to use some clinical data standards but not as broadly as was expected. The communities have not yet developed the specific technical approaches or the sustainable business models that will be required. Many communities are interested in creating an LHII and are developing the leadership commitment needed to translate that interest into an operational reality. Clinical information standards can be incorporated into a community's plans as often as they need to be. Communities have to overcome funding issues, develop deeper understanding of the technical and organizational issues, and aggressively share their learning to succeed within their community and to help other communities succeed. [Abstract/Link to Full Text]

Aronsky D, Ransom J, Robinson K
Accuracy of references in five biomedical informatics journals.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):225-8.
OBJECTIVE: To determine the rate and type of errors in biomedical informatics journal article references. METHODS: References in articles from the first 2004 issues of five biomedical informatics journals, Journal of the American Medical Informatics Association, Journal of Biomedical Informatics, International Journal of Medical Informatics, Methods of Information in Medicine, and Artificial Intelligence in Medicine were compared with MEDLINE for journal, authors, title, year, volume, and page number accuracy. If discrepancies were identified, the reference was compared with the original publication. Two reviewers independently evaluated each reference. RESULTS: The five journal issues contained 37 articles. Among the 656 eligible references, 225 (34.3%) included at least one error. Among the 225 references, 311 errors were identified. One or more errors were found in the bibliography of 31 (84%) of the 37 articles. The reference error rates by journal ranged from 22.1% to 40.7%. Most errors (39.0%) occurred in the author element, followed by the journal (31.2%), title (17.7%), page (7.4%), year (3.5%), and volume (1.3%) information. CONCLUSION: The study identified a considerable error rate in the references of five biomedical informatics journals. Authors are responsible for the accuracy of references and should more carefully check them, possibly using informatics-based assistance. [Abstract/Link to Full Text]

Stead WW, Kelly BJ, Kolodner RM
Achievable steps toward building a National Health Information infrastructure in the United States.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):113-20.
Consensus is growing that a health care information and communication infrastructure is one key to fixing the crisis in the United States in health care quality, cost, and access. The National Health Information Infrastructure (NHII) is an initiative of the Department of Health and Human Services receiving bipartisan support. There are many possible courses toward its objective. Decision makers need to reflect carefully on which approaches are likely to work on a large enough scale to have the intended beneficial national impacts and which are better left to smaller projects within the boundaries of health care organizations. This report provides a primer for use by informatics professionals as they explain aspects of that dividing line to policy makers and to health care leaders and front-line providers. It then identifies short-term, intermediate, and long-term steps that might be taken by the NHII initiative. [Abstract/Link to Full Text]

McCray AT
Promoting health literacy.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):152-63.
This report reviews some of the extensive literature in health literacy, much of it focused on the intersection of low literacy and the understanding of basic health care information. Several articles describe methods for assessing health literacy as well as methods for assessing the readability of texts, although generally these latter have not been developed with health materials in mind. Other studies have looked more closely at the mismatch between patients' literacy levels and the readability of materials intended for use by those patients. A number of studies have investigated the phenomenon of literacy from the perspective of patients' interactions in the health care setting, the disenfranchisement of some patients because of their low literacy skills, the difficulty some patients have in navigating the health care system, the quality of the communication between doctors and their patients including the cultural overlay of such exchanges, and ultimately the effect of low literacy on health outcomes. Finally, the impact of new information technologies has been studied by a number of investigators. There remain many opportunities for conducting further research to gain a better understanding of the complex interactions between general literacy, health literacy, information technologies, and the existing health care infrastructure. [Abstract/Link to Full Text]

Hripcsak G, Zhou L, Parsons S, Das AK, Johnson SB
Modeling electronic discharge summaries as a simple temporal constraint satisfaction problem.
J Am Med Inform Assoc. 2005 Jan-Feb;12(1):55-63.
OBJECTIVE: To model the temporal information contained in medical narrative reports as a simple temporal constraint satisfaction problem. DESIGN: A constraint satisfaction problem is defined by time points and constraints (inequalities between points). A time interval comprises a pair of points and a constraint. Five complete electronic discharge summaries and paragraphs from 226 other discharge summaries were studied. Medical events were represented as intervals, and assertions about events were represented as constraints. Through a consensus process, a set of encoding procedures and a list of issues related to encoding were generated. MEASUREMENTS: Instances of temporal disjunction and contradiction and distribution of temporal constraints were used. RESULTS: An average of 95 medical events (range, 46-151) and 234 temporal assertions (range, 118-388) were identified per complete discharge summary. Nondefinitional assertions were explicit (36%) or implicit (64%) and absolute (17%), qualitative (72%), or metric (11%). Implicit assertions were based on domain knowledge and assumptions, e.g., the section of the report determined the ordering of events. Issues included linking events, intermittence, periodicity, granularity, vagueness, ambiguity, uncertainty, and plans. ions such as intermittence were not represented explicitly. The temporal network was sparse: Only 0.80% (range, 0.42%-1.38%) of possible constraints were instantiated. No instances of discontinuous temporal disjunction were found in the complete summaries or the 226 paragraphs. One instance of temporal contradiction was found (intrareport rate of 0.2 with a 95% confidence interval of 0.005-1.114). CONCLUSION: A simple temporal constraint satisfaction problem appears sufficient to represent most temporal assertions in discharge summaries and may be useful for encoding electronic medical records. [Abstract/Link to Full Text]

Shapiro LG, Chung E, Detwiler LT, Mejino JL, Agoncillo AV, Brinkley JF, Rosse C
Processes and problems in the formative evaluation of an interface to the Foundational Model of Anatomy knowledge base.
J Am Med Inform Assoc. 2005 Jan-Feb;12(1):35-46.
The Digital Anatomist Foundational Model of Anatomy (FMA) is a large semantic network of more than 100,000 terms that refer to the anatomical entities, which together with 1.6 million structural relationships symbolically represent the physical organization of the human body. Evaluation of such a large knowledge base by domain experts is challenging because of the sheer size of the resource and the need to evaluate not just classes but also relationships. To meet this challenge, the authors have developed a relation-centric query interface, called Emily, that is able to query the entire range of classes and relationships in the FMA, yet is simple to use by a domain expert. Formative evaluation of this interface considered the ability of Emily to formulate queries based on standard anatomy examination questions, as well as the processing speed of the query engine. Results show that Emily is able to express 90% of the examination questions submitted to it and that processing time is generally 1 second or less, but can be much longer for complex queries. These results suggest that Emily will be a very useful tool, not only for evaluating the FMA, but also for querying and evaluating other large semantic networks. [Abstract/Link to Full Text]

Collmann J, Alaoui A, Nguyen D, Lindisch D
Safe teleradiology: information assurance as project planning methodology.
J Am Med Inform Assoc. 2005 Jan-Feb;12(1):84-9.
The Georgetown University Medical Center Department of Radiology used a tailored version of OCTAVE, a self-directed information security risk assessment method, to design a teleradiology system that complied with the regulation implementing the security provisions of the Health Insurance Portability and Accountability Act (HIPAA) of 1996. The system addressed threats to and vulnerabilities in the privacy and security of protected health information. By using OCTAVE, Georgetown identified the teleradiology program's critical assets, described threats to the assurance of those assets, developed and ran vulnerability scans of a system pilot, evaluated the consequences of security breaches, and developed a risk management plan to mitigate threats to program assets, thereby implementing good information assurance practices. This case study illustrates the basic point that prospective, comprehensive planning to protect the privacy and security of an information system strategically benefits program management as well as system security. [Abstract/Link to Full Text]

Lyons SS, Tripp-Reimer T, Sorofman BA, Dewitt JE, Bootsmiller BJ, Vaughn TE, Doebbeling BN
VA QUERI informatics paper: information technology for clinical guideline implementation: perceptions of multidisciplinary stakeholders.
J Am Med Inform Assoc. 2005 Jan-Feb;12(1):64-71.
OBJECTIVE: This multisite study compared the perceptions of three stakeholder groups regarding information technologies as barriers to and facilitators of clinical practice guidelines (CPGs). DESIGN: The study settings were 18 U.S. Veterans Affairs Medical Centers. A purposive sample of 322 individuals participated in 50 focus groups segmented by profession and included administrators, physicians, and nurses. Focus group participants were selected based on their knowledge of practice guidelines and involvement in facility-wide guideline implementation. MEASUREMENTS: Descriptive content analysis of 1,500 pages of focus group transcripts. RESULTS: Eighteen themes clustered into four domains. Stakeholders were similar in discussing themes in the computer function domain most frequently but divergent in other domains, with workplace factors more often discussed by administrators, system design issues discussed most by nurses, and personal concerns discussed by physicians and nurses. Physicians and nurses most often discussed barriers, whereas administrators focused most often on facilitation. Facilitators included guideline maintenance and charting formats. Barriers included resources, attitudes, time and workload, computer glitches, computer complaints, data retrieval, and order entry. Themes with dual designations included documentation, patient records, decision support, performance evaluation, CPG implementation, computer literacy, essential data, and computer accessibility. CONCLUSION: Stakeholders share many concerns regarding the relationships between information technologies and clinical guideline use. However, administrators, physicians, and nurses hold different opinions about specific facilitators and barriers. Health professionals' disparate perceptions could undermine guideline initiatives. Implementation plans should specifically incorporate actions to address these barriers and enhance the facilitative aspects of information technologies in clinical practice guideline use. [Abstract/Link to Full Text]

Zhao L, Lee KP, Hu J
Generating XML schemas for DICOM structured reporting templates.
J Am Med Inform Assoc. 2005 Jan-Feb;12(1):72-83.
In this paper, the authors describe a methodology to transform programmatically structured reporting (SR) templates defined by the Digital Imaging and Communications for Medicine (DICOM) standard into an XML schema representation. Such schemas can be used in the creation and validation of XML-encoded SR documents that use templates. Templates are a means to put additional constraints on an SR document to promote common formats for specific reporting applications or domains. As the use of templates becomes more widespread in the production of SR documents, it is important to ensure validity of such documents. The work described in this paper is an extension of the authors' previous work on XML schema representation for DICOM SR. Therefore, this paper inherits and partially modifies the structure defined in the earlier work. [Abstract/Link to Full Text]

Ohsfeldt RL, Ward MM, Schneider JE, Jaana M, Miller TR, Lei Y, Wakefield DS
Implementation of hospital computerized physician order entry systems in a rural state: feasibility and financial impact.
J Am Med Inform Assoc. 2005 Jan-Feb;12(1):20-7.
OBJECTIVE: The aim of this study was to estimate the costs of implementing computerized physician order entry (CPOE) systems in hospitals in a rural state and to evaluate the financial implications of statewide CPOE implementation. METHODS: A simulation model was constructed using estimates of initial and ongoing CPOE costs mapped onto all general hospitals in Iowa by bed quantity and current clinical information system (CIS) status. CPOE cost estimates were obtained from a leading CPOE vendor. Current CIS status was determined through mail survey of Iowa hospitals. Patient care revenue and operating cost data published by the Iowa Hospital Association were used to simulate the financial impact of CPOE adoption on hospitals. RESULTS: CPOE implementation would dramatically increase operating costs for rural and critical access hospitals in the absence of substantial costs savings associated with improved efficiency or improved patient safety. For urban and rural referral hospitals, the cost impact is less dramatic but still substantial. However, relatively modest benefits in the form of patient care cost savings or revenue enhancement would be sufficient to offset CPOE costs for these larger hospitals. CONCLUSION: Implementation of CPOE in rural or critical access hospitals may depend on net increase in operating costs. Adoption of CPOE may be financially infeasible for these small hospitals in the absence of increases in hospital payments or ongoing subsidies from third parties. [Abstract/Link to Full Text]

Carriero N, Osier MV, Cheung KH, Miller PL, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M
A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.
J Am Med Inform Assoc. 2005 Jan-Feb;12(1):90-8.
The rapid advances in high-throughput biotechnologies such as DNA microarrays and mass spectrometry have generated vast amounts of data ranging from gene expression to proteomics data. The large size and complexity involved in analyzing such data demand a significant amount of computing power. High-performance computation (HPC) is an attractive and increasingly affordable approach to help meet this challenge. There is a spectrum of techniques that can be used to achieve computational speedup with varying degrees of impact in terms of how drastic a change is required to allow the software to run on an HPC platform. This paper describes a high- productivity/low-maintenance (HP/LM) approach to HPC that is based on establishing a collaborative relationship between the bioinformaticist and HPC expert that respects the former's codes and minimizes the latter's efforts. The goal of this approach is to make it easy for bioinformatics researchers to continue to make iterative refinements to their programs, while still being able to take advantage of HPC. The paper describes our experience applying these HP/LM techniques in four bioinformatics case studies: (1) genome-wide sequence comparison using Blast, (2) identification of biomarkers based on statistical analysis of large mass spectrometry data sets, (3) complex genetic analysis involving ordinal phenotypes, (4) large-scale assessment of the effect of possible errors in analyzing microarray data. The case studies illustrate how the HP/LM approach can be applied to a range of representative bioinformatics applications and how the approach can lead to significant speedup of computationally intensive bioinformatics applications, while making only modest modifications to the programs themselves. [Abstract/Link to Full Text]

Simons WW, Mandl KD, Kohane IS
The PING personally controlled electronic medical record system: technical architecture.
J Am Med Inform Assoc. 2005 Jan-Feb;12(1):47-54.
Despite progress in creating standardized clinical data models and interapplication protocols, the goal of creating a lifelong health care record remains mired in the pragmatics of interinstitutional competition, concerns about privacy and unnecessary disclosure, and the lack of a nationwide system for authenticating and authorizing access to medical information. The authors describe the architecture of a personally controlled health care record system, PING, that is not institutionally bound, is a free and open source, and meets the policy requirements that the authors have previously identified for health care delivery and population-wide research. [Abstract/Link to Full Text]

Malin BA
An evaluation of the current state of genomic data privacy protection technology and a roadmap for the future.
J Am Med Inform Assoc. 2005 Jan-Feb;12(1):28-34.
The incorporation of genomic data into personal medical records poses many challenges to patient privacy. In response, various systems for preserving patient privacy in shared genomic data have been developed and deployed. Although these systems de-identify the data by removing explicit identifiers (e.g., name, address, or Social Security number) and incorporate sound security design principles, they suffer from a lack of formal modeling of inferences learnable from shared data. This report evaluates the extent to which current protection systems are capable of withstanding a range of re-identification methods, including genotype-phenotype inferences, location-visit patterns, family structures, and dictionary attacks. For a comparative re-identification analysis, the systems are mapped to a common formalism. Although there is variation in susceptibility, each system is deficient in its protection capacity. The author discovers patterns of protection failure and discusses several of the reasons why these systems are susceptible. The analyses and discussion within provide guideposts for the development of next-generation protection methods amenable to formal proofs. [Abstract/Link to Full Text]

Berner ES, Detmer DE, Simborg D
Will the wave finally break? A brief view of the adoption of electronic medical records in the United States.
J Am Med Inform Assoc. 2005 Jan-Feb;12(1):3-7.
For over thirty years, there have been predictions that the widespread clinical use of computers was imminent. Yet the "wave" has never broken. In this article, two broad time periods are examined: the 1960's to the 1980's and the 1980's to the present. Technology immaturity, health administrator focus on financial systems, application "unfriendliness," and physician resistance were all barriers to acceptance during the early time period. Although these factors persist, changes in clinicians' economics, more computer literacy in the general population, and, most importantly, changes in government policies and increased support for clinical computing suggest that the wave may break in the next decade. [Abstract/Link to Full Text]

Middleton B, Hammond WE, Brennan PF, Cooper GF
Accelerating U.S. EHR adoption: how to get there from here. recommendations based on the 2004 ACMI retreat.
J Am Med Inform Assoc. 2005 Jan-Feb;12(1):13-9.
Despite growing support for the adoption of electronic health records (EHR) to improve U.S. healthcare delivery, EHR adoption in the United States is slow to date due to a fundamental failure of the healthcare information technology marketplace. Reasons for the slow adoption of healthcare information technology include a misalignment of incentives, limited purchasing power among providers, variability in the viability of EHR products and companies, and limited demonstrated value of EHRs in practice. At the 2004 American College of Medical Informatics (ACMI) Retreat, attendees discussed the current state of EHR adoption in this country and identified steps that could be taken to stimulate adoption. In this paper, based upon the ACMI retreat, and building upon the experiences of the authors developing EHR in academic and commercial settings we identify a set of recommendations to stimulate adoption of EHR, including financial incentives, promotion of EHR standards, enabling policy, and educational, marketing, and supporting activities for both the provider community and healthcare consumers. [Abstract/Link to Full Text]

Ash JS, Bates DW
Factors and forces affecting EHR system adoption: report of a 2004 ACMI discussion.
J Am Med Inform Assoc. 2005 Jan-Feb;12(1):8-12.
After the first session of the American College of Medical Informatics 2004 retreat, during which the history of electronic health records was reviewed, the second session served as a forum for discussion about the state of the art of EHR adoption. Adoption and diffusion rates for both inpatient and outpatient EHRs are low for a myriad of reasons ranging from personal physician concerns about workflow to broad environmental issues. Initial recommendations for addressing these issues include providing communication and education to both providers and consumers and alignment of incentives for clinicians. [Abstract/Link to Full Text]

Waitman LR, Miller RA
Pragmatics of implementing guidelines on the front lines.
J Am Med Inform Assoc. 2004 Sep-Oct;11(5):436-8. [Abstract/Link to Full Text]

Shiffman RN, Michel G, Essaihi A, Thornquist E
Bridging the guideline implementation gap: a systematic, document-centered approach to guideline implementation.
J Am Med Inform Assoc. 2004 Sep-Oct;11(5):418-26.
OBJECTIVE: A gap exists between the information contained in published clinical practice guidelines and the knowledge and information that are necessary to implement them. This work describes a process to systematize and make explicit the translation of document-based knowledge into workflow-integrated clinical decision support systems. DESIGN: This approach uses the Guideline Elements Model (GEM) to represent the guideline knowledge. Implementation requires a number of steps to translate the knowledge contained in guideline text into a computable format and to integrate the information into clinical workflow. The steps include: (1) selection of a guideline and specific recommendations for implementation, (2) markup of the guideline text, (3) atomization, (4) deabstraction and (5) disambiguation of recommendation concepts, (6) verification of rule set completeness, (7) addition of explanations, (8) building executable statements, (9) specification of origins of decision variables and insertions of recommended actions, (10) definition of action types and selection of associated beneficial services, (11) choice of interface components, and (12) creation of requirement specification. RESULTS: The authors illustrate these component processes using examples drawn from recent experience translating recommendations from the National Heart, Lung, and Blood Institute's guideline on management of chronic asthma into a workflow-integrated decision support system that operates within the Logician electronic health record system. CONCLUSION: Using the guideline document as a knowledge source promotes authentic translation of domain knowledge and reduces the overall complexity of the implementation task. From this framework, we believe that a better understanding of activities involved in guideline implementation will emerge. [Abstract/Link to Full Text]

Gardner RM, Evans RS
Using computer technology to detect, measure, and prevent adverse drug events.
J Am Med Inform Assoc. 2004 Nov-Dec;11(6):535-6. [Abstract/Link to Full Text]

Hsieh TC, Kuperman GJ, Jaggi T, Hojnowski-Diaz P, Fiskio J, Williams DH, Bates DW, Gandhi TK
Characteristics and consequences of drug allergy alert overrides in a computerized physician order entry system.
J Am Med Inform Assoc. 2004 Nov-Dec;11(6):482-91.
OBJECTIVE: The aim of this study was to determine characteristics of drug allergy alert overrides, assess how often they lead to preventable adverse drug events (ADEs), and suggest methods for improving the allergy-alerting system. DESIGN: Chart review was performed on a stratified random subset of all allergy alerts occurring during a 3-month period (August through October 2002) at a large academic hospital. MEASUREMENTS: Factors that were measured were drug/allergy combinations that triggered alerts, frequency of specific override reasons, characteristics of ADEs, and completeness of allergy documentation. RESULTS: A total of 6,182 (80%) of 7,761 alerts were overridden in 1,150 patients. In this sample, only 10% of alerts were triggered by an exact match between the drug ordered and allergy listed. Physicians' most common reasons for overriding alerts were "Aware/Will monitor" (55%), "Patient does not have this allergy/tolerates" (33%), and "Patient taking already" (10%). In a stratified random subset of 320 patients (28% of 1,150) on chart review, 19 (6%) experienced ADEs attributed to the overridden drug; of these, 9 (47%) were serious. None of the ADEs was considered preventable, because the overrides were deemed clinically justifiable. The degree of completeness of patients' allergy lists was highly variable and generally low in both paper charts and the CPOE system. CONCLUSION: Overrides of drug-allergy alerts were common and about 1 in 20 resulted in ADEs, but all of the overrides resulting in ADEs appeared clinically justifiable. The high rate of alert overrides was attributable to frequent nonexact match alerts and infrequent updating of allergy lists. Based on these findings, we have made specific recommendations for increasing the specificity of alerting and thereby improving the clinical utility of the drug allergy alerting system. [Abstract/Link to Full Text]

Field TS, Gurwitz JH, Harrold LR, Rothschild JM, Debellis K, Seger AC, Fish LS, Garber L, Kelleher M, Bates DW
Strategies for detecting adverse drug events among older persons in the ambulatory setting.
J Am Med Inform Assoc. 2004 Nov-Dec;11(6):492-8.
OBJECTIVE: To examine various strategies for the identification of adverse drug events (ADEs) among older persons in the ambulatory clinical setting. DESIGN: A cohort study of Medicare enrollees (n = 31,757 per month) receiving medical care from a large multispecialty group practice during a 12-month observation period (July 1, 1999 through June 30, 2000). MEASUREMENTS: Possible drug-related incidents occurring in the ambulatory clinical setting were detected using signals from multiple sources. RESULTS: During the tracking period, there were 1,523 identified ADEs, of which 421 (28%) were considered preventable. Across all sources, 23,917 signals were found; 12,791 (53%) were potential incidents that led to review of a patient's medical record and 2,266 (9%) were presented to physician reviewers. Although the positive predictive value (PPV) for reports from providers was high compared with other sources (54%), only 11% of the ADEs and 6% of the preventable ADEs were identified through this source. PPVs for other sources ranged from a low of 4% for administrative incident reports to a high of 12% for free-text review of electronic notes. Computer-generated signals were the source for 31% of the ADEs and 37% of the preventable ADEs. Electronic notes were the source for 39% of the ADEs and 29% of the preventable ADEs. There was little overlap in the ADEs identified across all sources. CONCLUSION: Our findings emphasize the limitations of voluntary reporting by health care providers as the principal means for detection of ADEs and suggest that multiple strategies are required to detect ADEs in geriatric ambulatory patients. [Abstract/Link to Full Text]

Chang BL, Bakken S, Brown SS, Houston TK, Kreps GL, Kukafka R, Safran C, Stavri PZ
Bridging the digital divide: reaching vulnerable populations.
J Am Med Inform Assoc. 2004 Nov-Dec;11(6):448-57.
The AMIA 2003 Spring Congress entitled "Bridging the Digital Divide: Informatics and Vulnerable Populations" convened 178 experts including medical informaticians, health care professionals, government leaders, policy makers, researchers, health care industry leaders, consumer advocates, and others specializing in health care provision to underserved populations. The primary objective of this working congress was to develop a framework for a national agenda in information and communication technology to enhance the health and health care of underserved populations. Discussions during four tracks addressed issues and trends in information and communication technologies for underserved populations, strategies learned from successful programs, evaluation methodologies for measuring the impact of informatics, and dissemination of information for replication of successful programs. Each track addressed current status, ideal state, barriers, strategies, and recommendations. Recommendations of the breakout sessions were summarized under the overarching themes of Policy, Funding, Research, and Education and Training. The general recommendations emphasized four key themes: revision in payment and reimbursement policies, integration of health care standards, partnerships as the key to success, and broad dissemination of findings including specific feedback to target populations and other key stakeholders. [Abstract/Link to Full Text]

Hassol A, Walker JM, Kidder D, Rokita K, Young D, Pierdon S, Deitz D, Kuck S, Ortiz E
Patient experiences and attitudes about access to a patient electronic health care record and linked web messaging.
J Am Med Inform Assoc. 2004 Nov-Dec;11(6):505-13.
OBJECTIVE: Patient access to their electronic health care record (EHR) and Web-based communication between patients and providers can potentially improve the quality of health care, but little is known about patients' attitudes toward this combined electronic access. The objective of our study was to evaluate patients' values and perceptions regarding Web-based communication with their primary care providers in the context of access to their electronic health care record. METHODS: We conducted an online survey of 4,282 members of the Geisinger Health System who are registered users of an application (MyChart) that allows patients to communicate electronically with their providers and view selected portions of their EHR. To supplement the survey, we also conducted focus groups with 25 patients who were using the system and conducted one-on-one interviews with ten primary care clinicians. We collected and analyzed data on user satisfaction, ease of use, communication preferences, and the completeness and accuracy of the patient EHR. RESULTS: A total of 4,282 registered patient EHR users were invited to participate in the survey; 1,421 users (33%) completed the survey, 60% of them female. The age distribution of users was as follows: 18 to 30 (5%), 31 to 45 (24%), 46 to 64 (54%), 65 and older (16%). Using a continuous scale from 1 to 100, the majority of users indicated that the system was easy to use (mean scores ranged from 78 to 85) and that their medical record information was complete, accurate, and understandable (mean scores ranged from 65 to 85). Only a minority of users was concerned about the confidentiality of their information or about seeing abnormal test results after receiving only an explanatory electronic message from their provider. Patients preferred e-mail communication for some interactions (e.g., requesting prescription renewals, obtaining general medical information), whereas they preferred in-person communication for others (e.g., getting treatment instructions). Telephone or written communication was never their preferred communication channel. In contrast, physicians were more likely to prefer telephone communication and less likely to prefer e-mail communication. CONCLUSION: Patients' attitudes about the use of Web messaging and online access to their EHR were mostly positive. Patients were satisfied that their medical information was complete and accurate. A minority of patients was mildly concerned about the confidentiality and privacy of their information and about learning of abnormal test results electronically. Clinicians were less positive about using electronic communication than their patients. Patients and clinicians differed substantially regarding their preferred means of communication for different types of interactions. [Abstract/Link to Full Text]

Porter SC, Cai Z, Gribbons W, Goldmann DA, Kohane IS
The asthma kiosk: a patient-centered technology for collaborative decision support in the emergency department.
J Am Med Inform Assoc. 2004 Nov-Dec;11(6):458-67.
The authors report on the development and evaluation of a novel patient-centered technology that promotes capture of critical information necessary to drive guideline-based care for pediatric asthma. The design of this application, the asthma kiosk, addresses five critical issues for patient-centered technology that promotes guideline-based care: (1) a front-end mechanism for patient-driven data capture, (2) neutrality regarding patients' medical expertise and technical backgrounds, (3) granular capture of medication data directly from the patient, (4) formal algorithms linking patient-level semantics and asthma guidelines, and (5) output to both patients and clinical providers regarding best practice. The formative evaluation of the asthma kiosk demonstrates its ability to capture patient-specific data during real-time care in the emergency department (ED) with a mean completion time of 11 minutes. The asthma kiosk successfully links parents' data to guideline recommendations and identifies data critical to health improvements for asthmatic children that otherwise remains undocumented during ED-based care. [Abstract/Link to Full Text]

Mitchell JA, Fun J, McCray AT
Design of Genetics Home Reference: a new NLM consumer health resource.
J Am Med Inform Assoc. 2004 Nov-Dec;11(6):439-47.
The authors have developed the Genetics Home Reference, a consumer resource that addresses the health implications of the Human Genome Project. The research results made possible by the Human Genome Project are being made available increasingly in scientific databases on the Internet, but, because of the often highly technical nature of these databases, they are not readily accessible to the lay public. The authors' goal is to provide a bridge between the clinical questions of the public and the richness of the data emanating from the Human Genome Project. The Genetics Home Reference currently focuses on single gene or polygenic conditions that are also topics on MEDLINEplus, the National Library of Medicine's primary consumer health site. As knowledge of genetics expands, the interrelationships between genes and diseases will continue to unfold, and the site will reflect these developments. [Abstract/Link to Full Text]

Sneiderman CA, Ackerman MJ
Cellular radio telecommunication for health care: benefits and risks.
J Am Med Inform Assoc. 2004 Nov-Dec;11(6):479-81.
Cellular radio telecommunication has increased exponentially with many applications to health care reported. The authors attempt to summarize published applications with demonstrated effect on health care, review briefly the rapid evolution of hardware and software standards, explain current limitations and future potential of data quality and security, and discuss issues of safety. [Abstract/Link to Full Text]

Marenco L, Wang TY, Shepherd G, Miller PL, Nadkarni P
QIS: A framework for biomedical database federation.
J Am Med Inform Assoc. 2004 Nov-Dec;11(6):523-34.
Query Integrator System (QIS) is a database mediator framework intended to address robust data integration from continuously changing heterogeneous data sources in the biosciences. Currently in the advanced prototype stage, it is being used on a production basis to integrate data from neuroscience databases developed for the SenseLab project at Yale University with external neuroscience and genomics databases. The QIS framework uses standard technologies and is intended to be deployable by administrators with a moderate level of technological expertise: It comes with various tools, such as interfaces for the design of distributed queries. The QIS architecture is based on a set of distributed network-based servers, data source servers, integration servers, and ontology servers, that exchange metadata as well as mappings of both metadata and data elements to elements in an ontology. Metadata version difference determination coupled with decomposition of stored queries is used as the basis for partial query recovery when the schema of data sources alters. [Abstract/Link to Full Text]

Mayo NE, Poissant L, Ahmed S, Finch L, Higgins J, Salbach NM, Soicher J, Jaglal S
Incorporating the International Classification of Functioning, Disability, and Health (ICF) into an electronic health record to create indicators of function: proof of concept using the SF-12.
J Am Med Inform Assoc. 2004 Nov-Dec;11(6):514-22.
OBJECTIVE: The purpose of this proof-of-concept study was to assess the feasibility of using a generic health measure to create coded functional status indicators and compare the characterization of a stroke population using coded functional indicators and using health-related quality-of-life summary measures alone. DESIGN: Multiple raters assigned International Classification of Functioning, Disability, and Health (ICF) codes to the items of the 12-Item Short Form Health Survey (SF-12). Data for comparing the information from the SF-12 and from ICF codes were derived from the Montreal Stroke Cohort Study that was set up to examine the long-term impact of stroke. Available for analysis were data from 604 persons with stroke, average age 69 years, and 488 controls, average age 62 years. MEASUREMENT: The SF-12 provides two summary scores, one for physical health and one for mental health. Domains of the ICF are coded to three digits, before the decimal; specific categorizations of impairments, activity limitations, and participation restrictions are coded to four digits before the decimal. RESULTS: Persons with stroke scored, on average, approximately 10 points lower than controls on physical and mental health. The ICF coding indicated that this was attributed, not surprisingly, to greater difficulty in doing moderate activities including housework, climbing stairs, and working and was not attributed to differences in pain. Differences in mental health were attributed most strongly to greater fatigue (impairment in energy), but all areas of mental health were affected to some degree. CONCLUSION: The ICF coding provided enhanced functional status information in a format compatible with the structure of administrative health databases. [Abstract/Link to Full Text]

Dickerson S, Reinhart AM, Feeley TH, Bidani R, Rich E, Garg VK, Hershey CO
Patient Internet use for health information at three urban primary care clinics.
J Am Med Inform Assoc. 2004 Nov-Dec;11(6):499-504.
OBJECTIVE: To survey a cross section of patients presenting to three urban primary care clinics to understand online health information search behaviors. DESIGN AND ANALYSIS: At three urban primary care clinics affiliated with University at Buffalo, School of Medicine, 315 patients were interviewed. Interview questions included items on education, demographic information, employment, number of current prescriptions, insurance, online access, and specifics of health-searching behaviors. Chart review determined patient body mass index and number of chronic illnesses. Logistic regression and chi2 statistics were used to investigate the relationship between patient characteristics and the proportion of patients who use the Web for seeking health information. RESULTS: Approximately 53% of respondents reported using Web or e-mail in the past year and 68% (33% of total sample) of those who accessed the Web used it to search for health information. The two most commonly cited search areas included information about a physical illness and nutrition/fitness. Education and race significantly predicted online health-seeking behavior when considering all factors in the study. Many patients (22%) relied on friends and family to navigate the Web, and 45% of patients reported that the information that they sought was unrelated to their clinical visit. CONCLUSION: Current use of the Internet for health information was limited among more disadvantaged patient groups. More research is needed to examine the relationship between health-seeking behavior and patients' management of their health and well-being. [Abstract/Link to Full Text]

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Recent Articles in Journal of the Medical Library Association

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Epstein BA
A management case study: challenges of initiating an information service in molecular biology and genetics.
J Med Libr Assoc. 2006 Jul;94(3):245-7. [Abstract/Link to Full Text]

White P, Hall ME
Mapping the literature of case management nursing.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E99-106.
OBJECTIVES: Nursing case management provides a continuum of health care services for defined groups of patients. Its literature is multidisciplinary, emphasizing clinical specialties, case management methodology, and the health care system. This study is part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association. The study identifies core journals cited in case management literature and indexing services that access those journals. METHODS: Three source journals were identified based on established criteria, and cited references from each article published from 1997 to 1999 were analyzed. RESULTS: Nearly two-thirds of the cited references were from journals; others were from books, monographs, reports, government documents, and the Internet. Cited journal references were ranked in descending order, and Bradford's Law of Scattering was applied. The many journals constituting the top two zones reflect the diversity of this field. Zone 1 included journals from nursing administration, case management, general medicine, medical specialties, and social work. Two databases, PubMed/MEDLINE and OCLC ArticleFirst, provided the best indexing coverage. CONCLUSION: Collections that support case management require a relatively small group of core journals. Students and health care professionals will need to search across disciplines to identify appropriate literature. [Abstract/Link to Full Text]

Guenther JT
Mapping the literature of nursing informatics.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E92-8.
OBJECTIVE: This study was part of the Medical Library Association's Nursing and Allied Health Resources Section's project to map the nursing literature. It identified core journals in nursing informatics and the journals referenced in them and analyzed coverage of those journals in selected indexes. METHOD: Five core journals were chosen and analyzed for 1996, 1997, and 1998. The references in the core journal articles were examined for type and number of formats cited during the selected time period. Bradford's Law of Scattering divided the journals into frequency zones. RESULTS: The time interval, 1990 to 1998, produced 71% of the references. Internet references could not be tracked by date before 1990. Twelve journals were the most productive, 119 journals were somewhat productive, and 897 journals were the least productive. Journal of the American Medical Informatics Association was the most prolific core journal. The 1998 journal references were compared in CINAHL, PubMed/MEDLINE, Science Citation Index, and OCLC Article First. PubMed/MEDLINE had the highest indexing score. [Abstract/Link to Full Text]

Galganski CJ
Mapping the literature of nursing administration.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E87-91.
OBJECTIVES: As part of Phase I of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association, this study identifies the core literature cited in nursing administration and the indexing services that provide access to the core journals. The results of this study will assist librarians and end users searching for information related to this nursing discipline, as well as database producers who might consider adding specific titles to their indexing services. METHODS: Using the common methodology described in the overview article, five source journals for nursing administration were identified and selected for citation analysis over a three-year period, 1996 to 1998, to identify the most frequently cited titles according to Bradford's Law of Scattering. From this core of most productive journal titles, the bibliographic databases that provide the best access to these titles were identified. RESULTS: Results reveal that nursing administration literature relies most heavily on journal articles and on those titles identified as core nursing administrative titles. When the indexing coverage of nine services is compared, PubMed/MEDLINE and CINAHL provide the most comprehensive coverage of this nursing discipline. CONCLUSIONS: No one indexing service adequately covers this nursing discipline. Researchers needing comprehensive coverage in this area must search more than one database to effectively research their projects. While PubMed/MEDLINE and CINAHL provide more coverage for this discipline than the other indexing services, none is sufficiently broad in scope to provide indexing of nursing, health care management, and medical literature in a single file. Nurse administrators using the literature to research current work issues need to review not only the nursing titles covered by CINAHL but should also include the major weekly medical titles, core titles in health care administration, and general business sources if they wish to adequately cover the many aspects of nursing administration. [Abstract/Link to Full Text]

Seaton HJ
Mapping the literature of nurse-midwifery.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E80-6.
OBJECTIVE: This article is part of a project for mapping the literature of nursing. The purpose is to identify the core journals in nurse-midwifery and to determine the extent to which these titles are covered by standard indexing sources. METHODS: Cited references from two source journals were analyzed to discover the most frequently cited publications, including their format, age, and amount of dispersion, as well as the indexes that offer the most complete coverage. RESULTS: A study of the literature of nurse-midwifery reveals that the field is diverse, including such topics as women's health, obstetrics, gynecology, and parent-child relations, in addition to the practice of nurse-midwifery itself. Journals were the most heavily cited format, and analysis revealed that ten journals provided one-third of all the references in the study. CONCLUSIONS: A combination of Science Citation Index and Social Sciences Citation Index or PubMed/MEDLINE provided the best overall coverage because of the field's reliance on medical journals. CINAHL had the most complete coverage for the nurse-midwifery journals as well as nursing journals in general. [Abstract/Link to Full Text]

Allison MM
Mapping the literature of nephrology nursing.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E74-9.
OBJECTIVES: A bibliometric investigation was done to identify characteristics of the literature that nephrology nurses utilize. It is one component of a broader study, "Mapping the Literature of Nursing," by the Medical Library Association's Nursing and Allied Health Resources Section Task Force to Map the Literature of Nursing. METHODS: Following a standard protocol, this project utilized Bradford's Law of Scattering to analyze the literature of nephrology nursing. Citation analysis was done on articles that were published from 1996 to 1998 in a source journal. Cited journal titles were divided into three zones, and coverage in major article databases were scored for Zones 1 and 2. RESULTS: During the three-year period, journals were the most frequently cited format type. Eighty-one journals were cited in Zones 1 and 2. As Bradford's Law of Scattering predicted, a small number of the cited journals accounted for the most use. Coverage is most comprehensive for cited journals in Science Citation Index, PubMed/ MEDLINE, and EMBASE. When looking just at cited nursing journals, CINAHL and PubMed/MEDLINE provide the best indexing coverage. CONCLUSION: This study offers understanding of and insights into the types of information that nephrology nurses use for research. It is a valuable tool for anyone involved with providing nephrology nursing literature. [Abstract/Link to Full Text]

Taylor MK
Mapping the literature of medical-surgical nursing.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E65-73.
BACKGROUND: Medical-surgical or adult health nursing is a complex specialty that requires a wide-ranging literature to inform its research and practice. Several excellent qualitative aids exist for collection development for this field, but quantitative studies are few. While one bibliometric study of journals exists, no recent work had been done in this area. METHOD: The Mapping the Literature of Nursing Project protocol was used. Four source journals were selected, and a citation analysis of articles from 1996 to 1998 was conducted. RESULTS: A list of the most frequently cited journals was created, using Bradford's Law of Scattering. The list demonstrates that 1.2% of the cited medical-surgical nursing journals produced just over 33% of the citations. PubMed/MEDLINE, CINAHL, and Science Citation Index provided the most complete indexing coverage of all of the journals, with CINAHL providing the most complete coverage of nursing journals. Books were the second-most cited format. CONCLUSIONS: Citation analysis of journal articles is a useful aid for selecting journals for medical-surgical nursing collections, but it did not prove to be as useful for selecting materials in other formats. Indexes in addition to PubMed/MEDLINE are necessary to provide access to the journal literature serving this specialty. [Abstract/Link to Full Text]

Jacobs SK
Mapping the literature of maternal-child/gynecologic nursing.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E56-64.
OBJECTIVES: As part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association, this study identifies core journals cited in maternal-child/gynecologic nursing and the indexing services that access the cited journals. METHODS: Three source journals were selected and subjected to a citation analysis of articles from 1996 to 1998. RESULTS: Journals were the most frequently cited format (74.1%), followed by books (19.7%), miscellaneous (4.2%), and government documents (1.9%). Bradford's Law of Scattering was applied to the results, ranking cited journal references in descending order. One-third of the citations were found in a core of 14 journal titles; one-third were dispersed among a middle zone of 100 titles; and the remaining third were scattered in a larger zone of 1,194 titles. Indexing coverage for the core titles was most comprehensive in PubMed/MEDLINE, followed by Science Citation Index and CINAHL. CONCLUSION: The core of journals cited in this nursing specialty revealed a large number of medical titles, thus, the biomedical databases provide the best access. The interdisciplinary nature of maternal-child/ gynecologic nursing topics dictates that social sciences databases are an important adjunct. The study results will assist librarians in collection development, provide end users with guidelines for selecting databases, and influence database producers to consider extending coverage to identified titles. [Abstract/Link to Full Text]

Friedman Y
Mapping the literature of home health nursing.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E49-55.
OBJECTIVES: The purpose of this study was to identify core journals in home health nursing and to determine how well these journals were covered by indexing and abstracting services. The study was part of the project for mapping the nursing literature of the Medical Library Association's Nursing and Allied Health Resource Section. METHODS: A citation analysis of two core journals was done to determine distribution of references by format types and age of citations and dispersion of the literature, according to Bradford's Law of Scattering. The analysis of indexing coverage for Zone 1 and 2 was also provided. RESULTS: The study showed that 64.2% of citations came from journals, versus 22.9% from books and 12.9% from other publications. PubMed/ MEDLINE rated highest in average indexing coverage of Zone 1 and 2 journals, followed by CINAHL. PsycINFO, SocioAbstracts, and EBSCO Health Business FullTEXT showed practically no coverage for the home health nursing literature. CONCLUSION: As expected, journal articles were found to be the primary source for referencing and books, the secondary source. In regard to bibliographic control, no databases provided full coverage of the journals in the field of home health nursing. PubMed/MEDLINE and CINAHL gave better results in combination, because CINAHL tended to cover more nursing journals, while PubMed/MEDLINE did better with medical titles. [Abstract/Link to Full Text]

Allen MP, Levy JR
Mapping the general literature of American nursing.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E43-8.
OBJECTIVES: As part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association, this study identifies core journals cited by general or "popular" US nursing journals and the indexing services that cover the cited journals. METHODS: Three journals were selected for analysis: American Journal of Nursing, Nursing 96-98, and RN. The source journals were subjected to a citation analysis of articles from 1996 to 1998, followed by an analysis of database access to the most frequently cited journal titles. RESULTS: Cited formats included journals (63.7%), books (26.6%), government documents (3.0%), Internet (0.5%), and miscellaneous (6.2%). Cited references were relatively current; most (86.6%) were published in the current decade. One-third of the citations were found in a core of 24 journal titles; one-third were dispersed among a middle zone of 94 titles; and the remaining third were scattered in a larger zone of 694 titles. Indexing coverage for the core titles was most comprehensive in PubMed/MEDLINE, followed by CINAHL and Science Citation Index. CONCLUSIONS: Results support the popular (not scholarly) nature of these titles. While not a good source for original research, they fulfill a key role of disseminating nursing knowledge with their relevantly current citations to a broad variety of sources. [Abstract/Link to Full Text]

Murphy SC
Mapping the literature of transcultural nursing.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E143-51.
OVERVIEW: No bibliometric studies of the literature of the field of transcultural nursing have been published. This paper describes a citation analysis as part of the project undertaken by the Nursing and Allied Health Resources Section of the Medical Library Association to map the literature of nursing. OBJECTIVE: The purpose of this study was to identify the core literature and determine which databases provided the most complete access to the transcultural nursing literature. METHODS: Cited references from essential source journals were analyzed for a three-year period. Eight major databases were compared for indexing coverage of the identified core list of journals. RESULTS: This study identifies 138 core journals. Transcultural nursing relies on journal literature from associated health sciences fields in addition to nursing. Books provide an important format. Nearly all cited references were from the previous 18 years. In comparing indexing coverage among 8 major databases, 3 databases rose to the top. CONCLUSIONS: No single database can claim comprehensive indexing coverage for this broad field. It is essential to search multiple databases. Based on this study, PubMed/MEDLINE, Social Sciences Citation Index, and CINAHL provide the best coverage. Collections supporting transcultural nursing require robust access to literature beyond nursing publications. [Abstract/Link to Full Text]

Spasser MA, Weismantel A
Mapping the literature of rehabilitation nursing.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E137-42.
OBJECTIVE: This paper describes a citation analysis of the literature of rehabilitation nursing, conducted as part of the Medical Library Association's Nursing and Allied Health Section's the "Mapping the Literature of Nursing Project." METHODS: One core journal, Rehabilitation Nursing, was selected, being both the official journal of the Association of Rehabilitation Nurses and the only journal devoted exclusively to rehabilitation nursing. Citations were analyzed according to format and date and stratified according to Bradford's Law of Scattering. RESULTS: The nineteen journals that constitute Zone 1 contribute the same number of citations as the eighty-six journals that make up Zone 2. OCLC ArticleFirst, PubMed/MEDLINE, and CINAHL provide the most inclusive coverage of the rehabilitation literature. The source journal, Rehabilitation Nursing, is the most important journal in Zone 1 and thus the most influential rehabilitation nursing journal. Relative degrees of database coverage do not change between Zones 1 and 2. CONCLUSION: The journals in Zones 1 and 2 collectively represent most of the important subspecialties of rehabilitation nursing, such as the physiological, sociopsychological, and community reintegration issues involved in the long-term rehabilitation process. [Abstract/Link to Full Text]

Taylor MK
Mapping the literature of pediatric nursing.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E128-36.
BACKGROUND: Pediatric nurses work in an interdisciplinary field and face ever-increasing demands on their time and knowledge. Selection tools for librarians serving this group are available, but only one bibliometric analysis has examined citations to aid collection development. METHOD: The "Mapping the Literature of Nursing Project" protocol was used. Three source journals were selected, and a citation analysis of articles from 1998 to 2000 was conducted. RESULTS: The frequency of journal citation was tabulated, and a list of the most frequently cited journals was created. Just over 1% of the cited journals produced 33% of the citations. PubMed/MEDLINE, Science Citation Index, and Social Sciences Citation Index provided the most complete indexing coverage of all types of the journals, while CINAHL providing the most complete coverage of nursing journals. Books were the second-most frequently cited format. CONCLUSIONS: Citation analysis of journal articles from pediatric nursing journals may be helpful in selecting journals for libraries serving pediatric nurses and those who conduct pediatric nursing research. Librarians should consider adding indexes to their collection in addition to PubMed/MEDLINE to access the broad range of journals useful to this specialty. [Abstract/Link to Full Text]

Allen MP, Allison MM, Stevens S
Mapping the literature of nursing education.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E122-7.
OBJECTIVES: As part of a project to map the literature of nursing, sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association, this study identifies core journals cited in nursing education journals and the indexing services that cover the cited journals. METHODS: Three nursing education source journals were subjected to a citation analysis of articles from 1997 to 1999, followed by an analysis of database access to the most frequently cited journal titles. RESULTS: Cited formats included journals (62.4%), books (31.3%), government documents (1.4%), Internet (0.3%), and miscellaneous (4.6%). Cited references were relatively older than other studies, with just 58.6% published in the 1990s. One-third of the citations were found in a core of just 6 journal titles; one-third were dispersed among a middle zone of 53 titles; the remaining third were scattered in a larger zone of 762 titles. Indexing coverage for the core titles was most comprehensive in CINAHL, followed by PubMed/MEDLINE and Social Sciences Citation Index. CONCLUSIONS: Citation patterns in nursing education show more reliance on nursing and education literature than biomedicine. Literature searches need to include CINAHL and PubMed/MEDLINE, as well as education and social sciences databases. Likewise, library collections need to include education and social sciences resources to complement works developed for nurse educators. [Abstract/Link to Full Text]

Shams ML
Mapping the literature of nurse practitioners.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E114-21.
OBJECTIVES: This study was designed to identify core journals for the nurse practitioner specialty and to determine the extent of their indexing in bibliographic databases. METHODS: As part of a larger project for mapping the literature of nursing, this study followed a common methodology based on citation analysis. Four journals designated by nurse practitioners as sources for their practice information were selected. All cited references were analyzed to determine format types and publication years. Bradford's Law of Scattering was applied to identify core journals. Nine bibliographic databases were searched to estimate the index coverage of the core titles. RESULTS: The findings indicate that nurse practitioners rely primarily on journals (72.0%) followed by books (20.4%) for their professional knowledge. The majority of the identified core journals belong to non-nursing disciplines. This is reflected in the indexing coverage results: PubMed/MEDLINE more comprehensively indexes the core titles than CINAHL does. CONCLUSION: Nurse practitioners, as primary care providers, consult medical as well as nursing sources for their information. The implications of the citation analysis findings are significant for collection development librarians and indexing services. [Abstract/Link to Full Text]

Alpi KM
Mapping the literature of emergency nursing.
J Med Libr Assoc. 2006 Apr;94(2 Suppl):E107-13.
PURPOSE: Emergency nursing covers a broad spectrum of health care from trauma surgery support to preventive health care. The purpose of this study is to identify the core literature of emergency nursing and to determine which databases provide the most thorough indexing access to the literature cited in emergency nursing journals. This study is part of the Medical Library Association's Nursing and Allied Health Resources Section's project to map the nursing literature. METHODS: Four key emergency nursing journals were selected and subjected to citation analysis based on Bradford's Law of Scattering. RESULTS: A group of 12 journals made up 33.3% of the 7,119 citations, another 33.3% of the citations appeared in 92 journals, with the remaining 33.3% scattered across 822 journals. Three of the core 12 journals were emergency medicine titles, and 2 were emergency nursing titles from the selected source journals. Government publications constituted 7.5% of the literature cited. CONCLUSIONS: PubMed/MEDLINE provided the best overall indexing coverage for the journals, followed by CINAHL. However, CINAHL provided the most complete coverage for the source journals and the majority of the nursing and emergency medical technology publications and should be consulted by librarians and nurses seeking emergency nursing literature. [Abstract/Link to Full Text]

Whelan JS, Dvorkin L
Plants from many healing landscapes: gathering information and teaching clinicians about the cultural use of medicinal herbs.
J Med Libr Assoc. 2006 Apr;94(2):223-6. [Abstract/Link to Full Text]

Michel P, Mouillet E, Salmi LR
Comparison of Medical Subject Headings and standard terminology regarding performance of diagnostic tests.
J Med Libr Assoc. 2006 Apr;94(2):221-3. [Abstract/Link to Full Text]

Allen MP, Jacobs SK, Levy JR
Mapping the literature of nursing: 1996-2000.
J Med Libr Assoc. 2006 Apr;94(2):206-20.
INTRODUCTION: This project is a collaborative effort of the Task Force on Mapping the Nursing Literature of the Nursing and Allied Health Resources Section of the Medical Library Association. This overview summarizes eighteen studies covering general nursing and sixteen specialties. METHOD: Following a common protocol, citations from source journals were analyzed for a three-year period within the years 1996 to 2000. Analysis included cited formats, age, and ranking of the frequency of cited journal titles. Highly cited journals were analyzed for coverage in twelve health sciences and academic databases. RESULTS: Journals were the most frequently cited format, followed by books. More than 60% of the cited resources were published in the previous seven years. Bradford's law was validated, with a small core of cited journals accounting for a third of the citations. Medical and science databases provided the most comprehensive access for biomedical titles, while CINAHL and PubMed provided the best access for nursing journals.Discussion: Beyond a heavily cited core, nursing journal citations are widely dispersed among a variety of sources and disciplines, with corresponding access via a variety of bibliographic tools. Results underscore the interdisciplinary nature of the nursing profession. CONCLUSION: For comprehensive searches, nurses need to search multiple databases. Libraries need to provide access to databases beyond PubMed, including CINAHL and academic databases. Database vendors should improve their coverage of nursing, biomedical, and psychosocial titles identified in these studies. Additional research is needed to update these studies and analyze nursing specialties not covered. [Abstract/Link to Full Text]

Robu I, Robu V, Thirion B
An introduction to the Semantic Web for health sciences librarians.
J Med Libr Assoc. 2006 Apr;94(2):198-205.
OBJECTIVES: The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. METHODOLOGY: The paper is structured into two main parts. "Semantic Web Technology" provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. "Semantic Web Applications and Research Projects in the Biomedical Field" is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. DISCUSSION AND CONCLUSIONS: Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects. [Abstract/Link to Full Text]

Maccall SL
Clinical Digital Libraries Project: design approach and exploratory assessment of timely use in clinical environments.
J Med Libr Assoc. 2006 Apr;94(2):190-7.
OBJECTIVE: The paper describes and evaluates the use of Clinical Digital Libraries Project (CDLP) digital library collections in terms of their facilitation of timely clinical information seeking. DESIGN: A convenience sample of CDLP Web server log activity over a twelve-month period (7/2002 to 6/2003) was analyzed for evidence of timely information seeking after users were referred to digital library clinical topic pages from Web search engines. Sample searches were limited to those originating from medical schools (26% North American and 19% non-North American) and from hospitals or clinics (51% North American and 4% non-North American).Measurement: Timeliness was determined based on a calculation of the difference between the timestamps of the first and last Web server log "hit" during each search in the sample. The calculated differences were mapped into one of three ranges: less than one minute, one to three minutes, and three to five minutes. RESULTS: Of the 864 searches analyzed, 48% were less than 1 minute, 41% were 1 to 3 minutes, and 11% were 3 to 5 minutes. These results were further analyzed by environment (medical schools versus hospitals or clinics) and by geographic location (North America versus non-North American). Searches reflected a consistent pattern of less than 1 minute in these environments. Though the results were not consistent on a month-by-month basis over the entire time period, data for 8 of 12 months showed that searches shorter than 1 minute predominated and data for 1 month showed an equal number of less than 1 minute and 1 to 3 minute searches. CONCLUSIONS: The CDLP digital library collections provided timely access to high-quality Web clinical resources when used for information seeking in medical education and hospital or clinic environments from North American and non-North American locations and consistently provided access to the sought information within the documented two-minute standard. The limitations of the use of Web server data warrant an exploratory assessment. This research also suggests the need for further investigation in the area of timely digital library collection services to clinical environments. [Abstract/Link to Full Text]

Bowden VM, Wood FB, Warner DG, Olney CA, Olivier ER, Siegel ER
Health information Hispanic outreach in the Texas Lower Rio Grande Valley.
J Med Libr Assoc. 2006 Apr;94(2):180-9.
PURPOSE: This paper provides an overview of the two-year Texas Lower Rio Grande Valley Health Information Hispanic Outreach (HI HO) project. The project included a needs assessment, four pilot projects, and focus groups on the use of MedlinePlus and MedlinePlus en espaņol. The needs assessment included a survey of physicians' information usage and a review of the circuit librarian program that had been established in 1989. The pilot projects were located at a high school, a rural health clinic, an urban health clinic, and a community center. Diffusion of innovation theory provided a framework for interpreting the results of the pilot projects. METHODS: The survey of physicians' information usage partially replicated a similar 1990 survey. The review of the circuit librarian program included usage statistics, interviews of administrators, and a survey of participants. Pilot project methodology varied by site. At the high school, four students were trained to instruct their peers in the use of MedlinePlus. At the two clinics, a computer workstation was installed for patients to access MedlinePlus. At the community center, staff were trained to use MedlinePlus en espaņol to train community residents. Project evaluation included surveys, focus groups, and interviews. Indicators of success included increased level of consumer use of MedlinePlus, reports by key informants and consumers of how MedlinePlus was used, reports about training, and development of self-sustaining activity. RESULTS: The physician survey documented usage of health information resources in 2002 compared to 1990. The review of the circuit librarian program documented the change in program usage between 1989 and 2003. The pilot project at the high school was the most successful of the four pilot projects in introducing MedlinePlus to a large number of people, followed by the community center project. In the high school and community center projects, the participating institutions had reinforcing educational missions and paid staff who were highly motivated to achieve the project goals. The computer workstations projects at the two clinics were less successful, due in part to limited staff commitment and conflicting priorities. CONCLUSIONS: The HI HO project tested methods of reaching the Hispanic community in the Lower Rio Grande Valley region of Texas. The four HI HO pilot projects varied in achieving their stated objectives. But taken as a whole, the HI HO project significantly contributed to a better understanding of health information outreach to the Hispanic community, knowledge that should be useful to others with similar outreach activities. [Abstract/Link to Full Text]

Droese P, Peterson N
Utilization of the medical librarian in a state Medicaid program to provide information services geared to health policy and health disparities.
J Med Libr Assoc. 2006 Apr;94(2):174-9.
OBJECTIVE: The role of two solo medical librarians in supporting Medicaid programs by functioning as information specialists at regional and state levels is examined. SETTING: A solo librarian for the Massachusetts Medicaid (MassHealth) program and a solo librarian for the New England States Consortium Systems Organization (NESCSO) functioned as information specialists in context to support Medicaid policy development and clinical, administrative, and program staff for state Medicaid programs. BRIEF DESCRIPTION: The librarian for MassHealth initially focused on acquiring library materials and providing research support on culturally competent health care and outreach, as part of the United States Department of Health and Human Services Culturally and Linguistically Appropriate Services in Health Care Standards. The NESCSO librarian focused on state Medicaid system issues surrounding the implementation of the Health Insurance Portability and Accountability Act. The research focus expanded for both the librarians, shaping their roles to more directly support clinical and administrative policy development. Of note, the availability and dissemination of information to policy leaders facilitated efforts to reduce health disparities. In Massachusetts, this led to a state legislative special commission to eliminate health disparities, which released a report in November 2005. On a regional level, the NESCSO librarian provided opportunities for states in New England to share ideas and Medicaid program information. The Centers for Medicaid and Medicare are working with NESCSO to explore the potential for using the NESCSO model for collaboration for other regions of the United States. RESULTS/OUTCOMES: With the increased attention on evidence-based health care and reduction of health disparities, medical librarians are called on to support a variety of health care information needs. Nationally, state Medicaid programs are being called on to provide coverage and make complex medical decisions regarding the delivery of benefits. Increasing numbers of beneficiaries and shrinking Medicaid budgets demand effective and proactive decision making to provide quality care and to accomplish the missions of state Medicaid programs. In this environment, the opportunities for information professionals to provide value and knowledge management are increasing. [Abstract/Link to Full Text]

Dunn K, Crow SJ, Van Moorsel TG, Creazzo J, Tomasulo P, Markinson A
"Mini-Medical School for Librarians": from needs assessment to educational outcomes.
J Med Libr Assoc. 2006 Apr;94(2):166-73.
PURPOSE: This study evaluates the outcomes of the "Mini-Medical School for Librarians" or "Medical School Experience," a continuing education symposium designed to improve librarians' understanding of medicine and medical education. SUBJECTS: The subjects are the symposium participants, a group that consisted of fifty-eight medical librarians and other information professionals. METHODOLOGY: Pre- and post-symposium self-evaluation surveys gauged participants' self-assessed confidence with the course content. A follow-up survey was administered six months after the symposium. A learning action plan recorded both the intended and actual applications of course content to professional settings. RESULTS:T-test analysis of paired pre- and post-symposium responses reveal a significant positive change in the mean self-assessed confidence with course content immediately following the symposium. Pairings of post-symposium and follow-up survey responses indicate a slight reversal in attendees' confidence in the months following the symposium, but pairings of pre-symposium and follow-up survey results demonstrate that the longitudinal impact of the program on self-assessed confidence with course content was positive and significant. Analysis of the learning action plan revealed a disparity in how participants planned to use the information they learned in the course and how they actually used it. CONCLUSIONS: Continuing education programs that address the content and structure of medicine can be an effective means by which to inform both the novice's and mid-career medical librarian's understanding of medicine and medical education. [Abstract/Link to Full Text]

Scherrer CS, Dorsch JL, Weller AC
An evaluation of a collaborative model for preparing evidence-based medicine teachers.
J Med Libr Assoc. 2006 Apr;94(2):159-65.
PURPOSE: The authors studied the effectiveness of a train-the-trainer collaboration model between librarians and medical faculty to instruct librarians and health professionals in teaching evidence-based medicine (EBM) principles. METHODS: A telephone survey was administered to graduates of an EBM course who agreed to participate in the study. They were asked if and how they taught EBM on returning to their institutions, if they felt competent to critically appraise an article, if their skill in searching PubMed improved, and if they collaborated with others in teaching EBM. RESULTS: Most respondents were librarians. The class was successful in that most taught EBM on return to their home institutions. Most initiated collaboration with health professionals. The goals of improving PubMed searching and achieving statistical competency had less success. CONCLUSION: This model is effective in preparing librarians to teach EBM. Modeling and encouraging collaboration between librarians and health professionals were successful techniques. Librarians would like more instruction in statistical concepts and less in searching PubMed. conclusions cannot be made for health professionals because of the low response rate from this group. As evidence-based health care continues to extend to other disciplines, librarians can position themselves to participate fully in the EBM educational process. [Abstract/Link to Full Text]

Murphy SA
Consumer health information for pet owners.
J Med Libr Assoc. 2006 Apr;94(2):151-8.
OBJECTIVE: The author studied health information available for veterinary consumers both in print and online. METHODS: WorldCat was searched using a list of fifty-three Library of Congress subject headings relevant to veterinary consumer health to identify print resources for review. Identified items were then collected and assessed for authority, comprehensiveness of coverage, validity, and other criteria outlined by Rees. An in-depth assessment of the information available for feline lower urinary tract disease (FLUTD) and canine congestive heart failure (CHF) was then conducted to examine the availability and quality of information available for specific diseases and disorders. A reading grade level was assigned for each passage using the Flesch-Kincaid formula in the Readability Statistics feature in Microsoft Word. RESULTS/DISCUSSION: A total of 187 books and 7 Websites were identified and evaluated. More than half of the passages relating to FLUTD and CHF were written above an 11th-grade reading level. A limited quantity of quality, in-depth resources that address specific diseases and disorders and are written at an appropriate reading level for consumers is available. CONCLUSION: The library's role is to facilitate access to the limited number of quality consumer health resources that are available to veterinary consumers. [Abstract/Link to Full Text]

McKnight M
The information seeking of on-duty critical care nurses: evidence from participant observation and in-context interviews.
J Med Libr Assoc. 2006 Apr;94(2):145-51.
OBJECTIVES: An observational study describes on-duty nurses' informative behaviors from the perspective of library and information science, rather than patient care,. It reveals their information sources, the kinds of information they seek, and their barriers to information acquisition. METHODS: Participant observation and in-context interviews were used to record in detail fifty hours of the information behavior of a purposive sample of on-duty critical care nurses on twenty-bed critical care unit in a community hospital. The investigator used rigorous ethnographic methods-including open, in vivo, and axial coding--to analyze the resulting rich textual data. RESULTS: The nurses' information behavior centered on the patient, seeking information from people, the patient record, and other systems. The nurses mostly used patient-specific information, but they also used some social and logistic information. They occasionally sought knowledge-based information. Barriers to information acquisition included illegible handwriting, difficult navigation of online systems, equipment failure, unavailable people, social protocols, and mistakes caused by people multitasking while working with multiple complex systems. Although the participating nurses understood and respected evidence-based practice, many believed that taking time to read published information on duty was not only difficult, but perhaps also ethically wrong. They said that a personal information service available to them at all hours of the day or night would be very useful. CONCLUSIONS: On-duty critical care nursing is a patient-centric information activity. A major implication of this study for librarians is that immediate professional reference service--including quality and quantity filtering-may be more useful to on-duty nurses than do-it-yourself searching and traditional document delivery are. [Abstract/Link to Full Text]

Perley CM
Physician use of the curbside consultation to address information needs: report on a collective case study.
J Med Libr Assoc. 2006 Apr;94(2):137-44.
PURPOSE: The author reports key findings from a doctoral dissertation investigating what the curbside consultation is, how and why physicians use it, and what the implications for health sciences library services might be. SETTINGS/INFORMANTS: Primary informants included sixteen primary care physicians at six sites in one Midwestern state. Additional informants included twenty-eight specialists and subspecialists identified by the primary informants as colleagues who provided curbside consultations. METHODS: Qualitative research methods were used, including field observations, formal and informal interviews, and conversations with peer review physicians. RESULTS: Despite a lack of consensus about what constitutes a "good" curbside consultation, physician informants reported that curbside consultations were part of their medical education and that they continued to take part in them for a number of reasons. Tacit rules govern curbside consultation interactions, and negative consequences result when the rules are misunderstood or not observed. DISCUSSION/CONCLUSION: Acknowledging and understanding physicians' use of the curbside consultation to obtain and construct knowledge may suggest new ways for health sciences librarians to work with physicians in locating, diffusing, and disseminating clinical information. [Abstract/Link to Full Text]

Glanville JM, Lefebvre C, Miles JN, Camosso-Stefinovic J
How to identify randomized controlled trials in MEDLINE: ten years on.
J Med Libr Assoc. 2006 Apr;94(2):130-6.
OBJECTIVE: The researchers sought to assess whether the widely used 1994 Cochrane Highly Sensitive Search Strategy (HSSS) for randomized controlled trials (RCTs) in MEDLINE could be improved in terms of sensitivity, precision, or parsimony. METHODS: A gold standard of 1,347 RCT records and a comparison group of 2,400 non-trials were randomly selected from MEDLINE. Terms occurring in at least 1% of RCT records were identified. Fifty percent of the RCT and comparison group records were randomly selected, and the ability of the terms to discriminate RCTs from non-trial records was determined using logistic regression. The best performing combinations of terms were tested on the remaining records and in MEDLINE. RESULTS: The best discriminating term was "Clinical Trial" (Publication Type). In years where the Cochrane assessment of MEDLINE records had taken place, the strategies identified few additional unindexed records of trials. In years where Cochrane assessment has yet to take place, "Randomized Controlled Trial" (Publication Type) proved highly sensitive and precise. Adding six more search terms identified further, unindexed trials at reasonable levels of precision and with sensitivity almost equal to the Cochrane HSSS. CONCLUSIONS: Most reports of RCTs in MEDLINE can now be identified easily using "Randomized Controlled Trial" (Publication Type). More sensitive searches can be achieved by a brief strategy, the Centre for Reviews and Dissemination/Cochrane Highly Sensitive Search Strategy (2005 revision). [Abstract/Link to Full Text]

Wilczynski NL, McKibbon KA, Haynes RB
Response to Glanville et al.: How to identify randomized controlled trials in MEDLINE: ten years on.
J Med Libr Assoc. 2007 Apr;95(2):117-8; author reply 119-20. [Abstract/Link to Full Text]

Leclercq E
Response to Glanville et al.
J Med Libr Assoc. 2007 Apr;95(2):118-9; author reply 119-20. [Abstract/Link to Full Text]

Dudden RF, Corcoran K, Kaplan J, Magouirk J, Rand DC, Smith BT
The Medical Library Association Benchmarking Network: results.
J Med Libr Assoc. 2006 Apr;94(2):118-29.
OBJECTIVE: This article presents some limited results from the Medical Library Association (MLA) Benchmarking Network survey conducted in 2002. Other uses of the data are also presented. METHODS: After several years of development and testing, a Web-based survey opened for data input in December 2001. Three hundred eighty-five MLA members entered data on the size of their institutions and the activities of their libraries. The data from 344 hospital libraries were edited and selected for reporting in aggregate tables and on an interactive site in the Members-Only area of MLANET. The data represent a 16% to 23% return rate and have a 95% confidence level. RESULTS: Specific questions can be answered using the reports. The data can be used to review internal processes, perform outcomes benchmarking, retest a hypothesis, refute a previous survey findings, or develop library standards. The data can be used to compare to current surveys or look for trends by comparing the data to past surveys. CONCLUSIONS: The impact of this project on MLA will reach into areas of research and advocacy. The data will be useful in the everyday working of small health sciences libraries as well as provide concrete data on the current practices of health sciences libraries. [Abstract/Link to Full Text]

Dudden RF, Corcoran K, Kaplan J, Magouirk J, Rand DC, Smith BT
The Medical Library Association Benchmarking Network: development and implementation.
J Med Libr Assoc. 2006 Apr;94(2):107-17.
OBJECTIVE: This article explores the development and implementation of the Medical Library Association (MLA) Benchmarking Network from the initial idea and test survey, to the implementation of a national survey in 2002, to the establishment of a continuing program in 2004. Started as a program for hospital libraries, it has expanded to include other nonacademic health sciences libraries. METHODS: The activities and timelines of MLA's Benchmarking Network task forces and editorial board from 1998 to 2004 are described. RESULTS: The Benchmarking Network task forces successfully developed an extensive questionnaire with parameters of size and measures of library activity and published a report of the data collected by September 2002. The data were available to all MLA members in the form of aggregate tables. Utilization of Web-based technologies proved feasible for data intake and interactive display. A companion article analyzes and presents some of the data. MLA has continued to develop the Benchmarking Network with the completion of a second survey in 2004. CONCLUSIONS: The Benchmarking Network has provided many small libraries with comparative data to present to their administrators. It is a challenge for the future to convince all MLA members to participate in this valuable program. [Abstract/Link to Full Text]


Proceedings of the Symposium on Community-based Health Information Outreach, December 2-2, 2004, Bethesda, Maryland, USA.
J Med Libr Assoc. 2005 Oct;93(4 Suppl):S4-92. [Abstract/Link to Full Text]

Crumley ET
Exploring the roles of librarians and health care professionals involved with complementary and alternative medicine.
J Med Libr Assoc. 2006 Jan;94(1):81-9.
OBJECTIVES: The researcher conducted qualitative research about the role of health care professionals and librarians involved with complementary and alternative medicine (CAM). The goals were to identify resources these professionals use to explore the librarians' role as well as their approaches to teaching and searching with respect to CAM, to acquire information about CAM education, and to connect with other librarians in the CAM field. METHODS: Semi-structured interviews with open-ended questions were used. RESULTS: Sixteen health care and information professionals from ten different institutions in Boston, Baltimore, and Calgary were interviewed. Major themes from the interviews were: CAM funding, integration of CAM and conventional medicine, roles of librarians, "hot" CAM issues, and information access. Information about four aspects of CAM education--technology, undergraduate, graduate, and continuing--is presented. A wealth of information resources was identified. CONCLUSIONS: A CAM librarian's role is unique; many specialize in specific areas of CAM, and opportunities exist for librarians to partner with CAM groups. CAM information professionals' major roles involve information access and retrieval and education. Further study is required concerning CAM consumer health, integrative CAM and conventional medicine models, and the librarian's role in a CAM environment. CAM funding is a major concern. [Abstract/Link to Full Text]

MacCall SL
Online medical books: their availability and an assessment of how health sciences libraries provide access on their public Websites.
J Med Libr Assoc. 2006 Jan;94(1):75-80.
OBJECTIVE: The objective of this study was to determine the number and topical range of available online medical books and to assess how health sciences libraries were providing access to these resources on their public Websites. METHOD: The collection-based evaluative technique of list checking was used to assess the number and topical range of online medical books of the six largest publishers. Publisher inventory lists were downloaded over a two-day period (May 16-17, 2004). Titles were counted and compared with the 2003 Brandon/Hill list. A sample of health sciences libraries was subsequently derived by consulting the 2004 "Top Medical Schools-Research" in U.S. News & World Report. Bibliographic and bibliothecal access methods were evaluated based on an inspection of the publicly available Websites of the sample libraries. RESULTS: Of 318 currently published online medical books, 151 (47%) were Brandon/Hill titles covering 42 of 59 Brandon/Hill topics (71%). These 151 titles represented 22% (N = 672) of the Brandon/Hill list, which further broke down as 52 minimal core, 41 initial purchase, and 58 other recommended Brandon/Hill titles. These numbers represented 50%, 28%, and 12%, respectively, of all Brandon/Hill titles corresponding to those categories. In terms of bibliographic access, 20 of 21 of sampled libraries created catalog records for their online medical books, 1 of which also provided analytical access at the chapter level, and none provided access at the chapter section level. Of the 21 libraries, 19 had library Website search engines that provided title-level access and 4 provided access at the chapter level and none that at the chapter section level. For bibliothecal access, 19 of 21 libraries provided title-level access to medical books, 8 of which provided classified and alphabetic arrangements, 1 provided a classified arrangement only, and 10 provided an alphabetic arrangement only. No library provided a bibliothecal arrangement for medical book chapters or chapter sections. CONCLUSIONS: This study shows that the number and topical range of online medical books is reaching a point where collection-level consideration is warranted to facilitate efficient use and to prevent the problem of split files. However, the results also show that few efforts are underway on the publicly available Websites of the surveyed health sciences libraries to provide the analytical access necessary to meet the structural needs of clinical information seekers. [Abstract/Link to Full Text]

Burrows S
A review of electronic journal acquisition, management, and use in health sciences libraries.
J Med Libr Assoc. 2006 Jan;94(1):67-74.
PURPOSE: The paper describes patterns of electronic journal usage in health sciences libraries during the past decade. METHOD: The paper presents a case study, documenting the pattern of acquisition, management, and usage at the Louis Calder Memorial Library of the University of Miami Miller School of Medicine. RESULTS: Health sciences journals were early to offer electronic alternatives to print. As a result, health sciences libraries, their patrons, and the public at large were early to embrace the new versions and continue to embrace the significant changes in scholarly communication they enable. Although the patterns of electronic journals among health sciences libraries and other special and academic libraries have similarities, they also have differences. Broad studies of electronic journals in non-health sciences libraries have been published, but a retrospective review of electronic journals in health sciences libraries has not. [Abstract/Link to Full Text]

Shedlock J, Walton LJ
Developing a virtual community for health sciences library book selection: Doody's Core Titles.
J Med Libr Assoc. 2006 Jan;94(1):61-6.
PURPOSE: The purpose of this article is to describe Doody's Core Titles in the Health Sciences as a new selection guide and a virtual community based on an effective use of online systems and to describe its potential impact on library collection development. SETTING/PARTICIPANTS/RESOURCES: The setting is the availability of health sciences selection guides. Participants include Doody Enterprise staff, Doody's Library Board of Advisors, content specialists, and library selectors. Resources include the online system used to create Doody's Core Titles along with references to complementary databases. BRIEF DESCRIPTION: Doody's Core Titles is described and discussed in relation to the literature of selection guides, especially in comparison to the Brandon/Hill selected lists that were published from 1965 to 2003. Doody's Core Titles seeks to fill the vacuum created when the Brandon/Hill lists ceased publication. Doody's Core Titles is a unique selection guide based on its method of creating an online community of experts to identify and score a core list of titles in 119 health sciences specialties and disciplines. RESULTS/OUTCOME: The result is a new selection guide, now available annually, that will aid health sciences librarians in identifying core titles for local collections. EVALUATION METHOD: Doody's Core Titles organizes the evaluation of core titles that are identified and recommended by content specialists associated with Doody's Book Review Service and library selectors. A scoring mechanism is used to create the selection of core titles, similar to the star rating system employed in other Doody Enterprise products and services. [Abstract/Link to Full Text]

Coumou HC, Meijman FJ
How do primary care physicians seek answers to clinical questions? A literature review.
J Med Libr Assoc. 2006 Jan;94(1):55-60.
OBJECTIVES: The authors investigated the extent to which changes occurred between 1992 and 2005 in the ways that primary care physicians seek answers to clinical problems. What search strategies are used? How much time is spent on them? How do primary care physicians evaluate various search activities and information sources? Can a clinical librarian be useful to a primary care physician? METHODS: Twenty-one original research papers and three literature reviews were examined. No systematic reviews were identified. RESULTS: Primary care physicians seek answers to only a limited number of questions about which they first consult colleagues and paper sources. This practice has basically not changed over the years despite the enormous increase in and better accessibility to electronic information sources. One of the major obstacles is the time it takes to search for information. Other difficulties primary care physicians experience are related to formulating an appropriate search question, finding an optimal search strategy, and interpreting the evidence found. Some studies have been done on the supporting role of a clinical librarian in general practice. However, the effects on professional behavior of the primary care physician and on patient outcome have not been studied. A small group of primary care physicians prefer this support to developing their own search skills. DISCUSSION: Primary care physicians have several options for finding quick answers: building a question-and-answer database, consulting filtered information sources, or using an intermediary such as a clinical librarian. [Abstract/Link to Full Text]

Wessel CB, Tannery NH, Epstein BA
Information-seeking behavior and use of information resources by clinical research coordinators.
J Med Libr Assoc. 2006 Jan;94(1):48-54.
PURPOSE: The study sought to understand the literature searching experiences and skills of clinical research coordinators at a large academic medical center. SETTING/PARTICIPANTS/RESOURCES: The Health Sciences Library System, University of Pittsburgh, conducted a survey of clinical research coordinators at the University of Pittsburgh and the University of Pittsburgh Medical Center to solicit their perceived use and knowledge of the library's electronic resources. BRIEF DESCRIPTION: The University of Pittsburgh Institutional Review Board (IRB) is a "high volume IRB" that monitors human subject research at both the University of Pittsburgh and the University of Pittsburgh Medical Center. More than 3,500 human research studies and clinical trials are active at any given time. Many studies entail more than minimal risk to human subjects, with the majority evaluating or including a drug or medical device. Clinical research coordinators are involved in most of these studies or trials. Their roles and responsibilities focus on managing many aspects of the study or clinical trial. As a first step in understanding the literature searching experiences and skills of these research coordinators, baseline data were gathered from this group in November 2004. RESULTS/OUTCOME: The data from this survey indicate that clinical research coordinators are a population who would benefit from training by academic medical center librarians in how to use electronic library resources and services. EVALUATION METHOD: A Web-based survey solicited participants' information (gender, education, job title) and role in the IRB process (job responsibilities, number studies they manage). The majority of the survey questions focused on the use of specific electronic library resources, the type of information wanted, and the types of problems encountered. [Abstract/Link to Full Text]

Wong SS, Wilczynski NL, Haynes RB
Developing optimal search strategies for detecting clinically sound treatment studies in EMBASE.
J Med Libr Assoc. 2006 Jan;94(1):41-7.
OBJECTIVE: The ability to accurately identify articles about therapy in large bibliographic databases such as EMBASE is important for researchers and clinicians. Our study aimed to develop optimal search strategies for detecting sound treatment studies in EMBASE in the year 2000. METHODS: Hand searches of journals were compared with retrievals from EMBASE for candidate search strategies. Six trained research assistants reviewed fifty-five journals indexed in EMBASE and rated articles using purpose and quality indicators. Candidate search strategies were developed for identifying treatment articles and then tested, and the retrievals were compared with the hand-search data. The operating characteristics of the strategies were calculated. RESULTS: Three thousand eight hundred fifty articles were original studies on treatment, of which 1,256 (32.6%) were methodologically sound. Combining search terms revealed a top performing strategy (random:.tw. OR clinical trial:.mp. OR exp health care quality) with sensitivity of 98.9% and specificity of 72.0%. Maximizing specificity, a top performing strategy (double-blind:.mp. OR placebo:.tw. OR blind: .tw.) achieved a value over 96.0%, but with compromised sensitivity at 51.7%. A 3-term strategy achieved the best optimization of sensitivity and specificity (random:.tw. OR placebo:.mp. OR double-blind:.tw.), with both these values over 92.0%. CONCLUSION: Search strategies can achieve high performance for retrieving sound treatment studies in EMBASE. [Abstract/Link to Full Text]