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Recent Articles in Journal of Medical Internet Research

Hartmann CW, Sciamanna CN, Blanch DC, Mui S, Lawless H, Manocchia M, Rosen RK, Pietropaoli A
A website to improve asthma care by suggesting patient questions for physicians: qualitative analysis of user experiences.
J Med Internet Res. 2007;9(1):e3.
BACKGROUND: Asthma is one of the most prevalent chronic conditions in the United States, yet despite the existence of national guidelines, nearly three fourths of patients with asthma do not have adequate control and clinical adherence to guidelines is low. While there are many reasons for this, physician inertia with respect to treatment change is partly to blame. Research suggests that patients who ask for specific tests and treatments are more likely to receive them. OBJECTIVES: This study investigated the impact and experience of using an interactive patient website designed to give patients individual feedback about their condition and to suggest tailored questions for patients to ask their physician. The website was designed to be used prior to a physician visit, to increase the likelihood that patients would receive recommended tests and treatments. METHODS: A total of 37 adult patients with asthma participated in semi-structured telephone interviews aimed at eliciting information about their experiences with the website. Transcripts were coded using qualitative data analysis techniques and software. Themes were developed from subsets of codes generated through the analysis. In addition, 26 physicians were surveyed regarding their impressions of the website. RESULTS: Opportunities exist for improving website feedback, although the majority of both patient and physician respondents held favorable opinions about the site. Two major themes emerged regarding patients' experiences with the website. First, many patients who used the website had a positive shift in their attitudes regarding interactions with their physicians. Second, use of the website prompted patients to become more actively involved in their asthma care. No patient reported any negative experiences as a result of using the website. Physicians rated the website positively. CONCLUSIONS: Patients perceived that the interactive website intervention improved communication and interaction with their physicians, suggesting that patients can play a role in overcoming the clinical inertia of providers. Although the design and content of the website can be improved upon, the main findings suggest that use of the website is well accepted and is perceived to improve the quality of care that patients receive. [Abstract/Link to Full Text]

Vallejo MA, Jord�n CM, D�az MI, Comeche MI, Ortega J
Psychological assessment via the internet: a reliability and validity study of online (vs paper-and-pencil) versions of the General Health Questionnaire-28 (GHQ-28) and the Symptoms Check-List-90-Revised (SCL-90-R).
J Med Internet Res. 2007;9(1):e2.
BACKGROUND: Internet psychology services are rapidly increasing and that implies online assessment. To guarantee the results of these new online evaluation procedures, it is necessary to have reliable and valid assessment tools. OBJECTIVE: In this work we analyzed the online versions of two popular psychopathology screening questionnaires: the General Health Questionnaire-28 (GHQ-28) and the Symptoms Check-List-90-Revised (SCL-90-R). METHODS: A total of 185 psychology students were recruited from two universities in Madrid, Spain. All of them had Internet access at home. A test-retest situation and factorial analysis were used to generate reliability and validity data. Both paper-and-pencil questionnaires (test) and their online versions (retest) were completed by 100 participants (median gap = 17 days). RESULTS: Results suggest that both online questionnaires were fairly equivalent to their paper-and-pencil versions, with higher reliability values for the SCL-90-R. Factorial analysis tended to reproduce the structure shown in former investigations of both questionnaires, replicating the four-factor structure of the GHQ-28 but failing to do so with the nine-factor structure of the SCL-90-R. Instead, a large unrotated factor appeared. CONCLUSIONS: Further research should be carried out to confirm these data, but our work supports the online use of both assessment tools. The psychometric properties of the online version of GHQ-28 is similar to the paper-and-pencil and we can recommend its utilization in a Web environment. In contrast, SCL-90-R can only be recommended as a global index for psychological distress, using the Global Severity Index (GSI), not necessarily its subscales; and it should be considered that the online scores were lower than the ones with the paper-and-pencil version. [Abstract/Link to Full Text]

Verheijden MW, Jans MP, Hildebrandt VH, Hopman-Rock M
Rates and determinants of repeated participation in a web-based behavior change program for healthy body weight and healthy lifestyle.
J Med Internet Res. 2007;9(1):e1.
BACKGROUND: In recent years, many tailored lifestyle counseling programs have become available through the Internet. Previous research into such programs has shown selective enrollment of relatively healthy people. However, because of the known dose-response relationship between the intensity and frequency of counseling and the behavior change outcomes, selective retention may also be a concern. OBJECTIVE: The aim of this study was to identify rates and determinants of repeat participation in a Web-based health behavior change program. METHODS: A Web-based health behavior change program aimed to increase people's awareness of their own lifestyle, to promote physical activity, and to prevent overweight and obesity was available on the Internet from July 2004 onward at no cost. Univariate and multivariate logistic regression analyses were conducted to identify characteristics of people who participated in the program more than once. Age, compliance with physical activity guidelines, body mass index, smoking status, and the consumption of fruit, vegetables, and alcohol were included in the analyses. RESULTS: A total of 9774 people participated in the baseline test, of which 940 used the site more than once (9.6%). After exclusion of individuals with incomplete data, 6272 persons were included in the analyses. Of these 6272 people, 5560 completed only the baseline test and 712 also participated in follow-up. Logistic regression predicting repeated use determined that older individuals were more likely to participate in follow-up than people aged 15-20 years. The odds ratios for the age categories 41-50, 51-60, and > 60 years were 1.40 (95% CI = 1.02-1.91), 1.43 (95% CI = 1.02-2.01), and 1.68 (95% CI = 1.03-2.72), respectively. Individuals who never smoked were more likely to participate repeatedly than current smokers and ex-smokers (OR = 1.44, 95% CI = 1.14-1.82 and OR = 1.49, 95% CI = 1.17-1.89, respectively). People meeting the guidelines for physical activity of moderate intensity (OR = 1.23 95% CI = 1.04-1.46) and for vegetable consumption (OR = 1.26 95% CI = 1.01-1.57) were also more likely to participate repeatedly than people who did not, as were obese people compared to individuals with normal weight (OR = 1.41 95% CI = 1.09-1.82). CONCLUSIONS: For some variables, this study confirms our concern that behavioral intervention programs may reach those who need them the least. However, contrary to most expectations, we found that obese people were more likely to participate in follow-up than people of normal body weight. The non-stigmatizing way of addressing body weight through the Internet may be part of the explanation for this. Our findings suggest that Web-based health behavior change programs may be more successful in the area of weight management than in many other health-related areas. They also stress the importance of adequate coverage of weight management in Web-based health promotion programs, as a driver to continue participation for overweight and obese people. [Abstract/Link to Full Text]

Hurling R, Catt M, Boni MD, Fairley BW, Hurst T, Murray P, Richardson A, Sodhi JS
Using internet and mobile phone technology to deliver an automated physical activity program: randomized controlled trial.
J Med Internet Res. 2007;9(2):e7.
BACKGROUND: The Internet has potential as a medium for health behavior change programs, but no controlled studies have yet evaluated the impact of a fully automated physical activity intervention over several months with real-time objective feedback from a monitor. OBJECTIVE: The aim was to evaluate the impact of a physical activity program based on the Internet and mobile phone technology provided to individuals for 9 weeks. METHODS: A single-center, randomized, stratified controlled trial was conducted from September to December 2005 in Bedfordshire, United Kingdom, with 77 healthy adults whose mean age was 40.4 years (SD = 7.6) and mean body mass index was 26.3 (SD = 3.4). Participants were randomized to a test group that had access to an Internet and mobile phone-based physical activity program (n = 47) or to a control group (n = 30) that received no support. The test group received tailored solutions for perceived barriers, a schedule to plan weekly exercise sessions with mobile phone and email reminders, a message board to share their experiences with others, and feedback on their level of physical activity. Both groups were issued a wrist-worn accelerometer to monitor their level of physical activity; only the test group received real-time feedback via the Internet. The main outcome measures were accelerometer data and self-report of physical activity. RESULTS: At the end of the study period, the test group reported a significantly greater increase over baseline than did the control group for perceived control (P < .001) and intention/expectation to exercise (P < .001). Intent-to-treat analyses of both the accelerometer data (P = .02) and leisure time self-report data (P = .03) found a higher level of moderate physical activity in the test group. The average increase (over the control group) in accelerometer-measured moderate physical activity was 2 h 18 min per week. The test group also lost more percent body fat than the control group (test group: -2.18, SD = 0.59; control group: -0.17, SD = 0.81; P = .04). CONCLUSIONS: A fully automated Internet and mobile phone-based motivation and action support system can significantly increase and maintain the level of physical activity in healthy adults. [Abstract/Link to Full Text]

Beaudin JS, Intille SS, Morris ME
To track or not to track: user reactions to concepts in longitudinal health monitoring.
J Med Internet Res. 2006;8(4):e29.
BACKGROUND: Advances in ubiquitous computing, smart homes, and sensor technologies enable novel, longitudinal health monitoring applications in the home. Many home monitoring technologies have been proposed to detect health crises, support aging-in-place, and improve medical care. Health professionals and potential end users in the lay public, however, sometimes question whether home health monitoring is justified given the cost and potential invasion of privacy. OBJECTIVE: The aim of the study was to elicit specific feedback from health professionals and laypeople about how they might use longitudinal health monitoring data for proactive health and well-being. METHODS: Interviews were conducted with 8 health professionals and 26 laypeople. Participants were asked to evaluate mock data visualization displays that could be generated by novel home monitoring systems. The mock displays were used to elicit reactions to longitudinal monitoring in the home setting as well as what behaviors, events, and physiological indicators people were interested in tracking. RESULTS: Based on the qualitative data provided by the interviews, lists of benefits of and concerns about health tracking from the perspectives of the practitioners and laypeople were compiled. Variables of particular interest to the interviewees, as well as their specific ideas for applications of collected data, were documented. CONCLUSIONS: Based upon these interviews, we recommend that ubiquitous "monitoring" systems may be more readily adopted if they are developed as tools for personalized, longitudinal self-investigation that help end users learn about the conditions and variables that impact their social, cognitive, and physical health. [Abstract/Link to Full Text]

Knaevelsrud C, Maercker A
Does the quality of the working alliance predict treatment outcome in online psychotherapy for traumatized patients?
J Med Internet Res. 2006;8(4):e31.
BACKGROUND: The provision of online counseling and online therapy is steadily increasing. The results of a number of controlled trials investigating the efficacy of online approaches indicate that some of these new treatment alternatives might indeed be effective. Yet, little is known about how the therapeutic relationship (or working alliance) evolves over the Internet and whether it influences treatment outcome as it does in traditional face-to-face therapy. The working alliance has been defined as the extent to which a patient and a therapist work collaboratively and purposefully and connect emotionally. OBJECTIVE: The aim of the study was to investigate the quality and predictive relevance of the therapeutic alliance for patients receiving a short-term, Internet-based, cognitive-behavioral therapy program for posttraumatic stress reactions. METHODS: After rigorous screening for exclusion criteria of high dissociative tendencies, risk of psychosis, and suicidal tendencies, 48 patients, who had experienced a traumatic event in the past, were included in the online treatment study. The short form of the Working Alliance Inventory (WAI-S) was administered at the fourth treatment session. The relevance of the therapeutic relationship for treatment outcome was assessed in terms of residual gain from pretreatment assessment to the end of treatment. The revised Impact of Event Scale (IES-R) and the depression and anxiety subscales of the Brief Symptom Inventory (BSI) were used to assess treatment outcome. RESULTS: A total of 48 participants were included in the analysis. Overall, high alliance scores were found. In contrast to previous studies of conventional face-to-face therapy, there was only a low to modest association (.13 to .33) between the quality of the therapeutic relationship and treatment outcome. CONCLUSION: High alliance scores indicate that it was possible to establish a stable and positive therapeutic relationship online. However, the therapeutic relationship was found to be a less relevant predictor of the therapy outcome than in face-to-face approaches. We discuss whether this finding can be attributed to methodological reasons such as the restricted range of alliance ratings obtained or the time of administration of the WAI-S, or whether the therapeutic relationship might be less relevant to the treatment outcome of online therapy approaches. [Abstract/Link to Full Text]

Levin E, Levin A
Evaluation of spoken dialogue technology for real-time health data collection.
J Med Internet Res. 2006;8(4):e30.
BACKGROUND: A real-time assessment of patients' experiences is an important methodology for studies in health care, quality of life, behavioral sciences, and new drug and treatment development. Ecological momentary assessment is a methodology that allows for real-time assessment of experience and behavior in a subject's natural environment. Recently, electronic data collection techniques have been introduced, including systems utilizing interactive voice response. OBJECTIVE: The objective of this project was evaluation of spoken dialogue methodology for real-time data collection of information from patients for health, behavioral, and lifestyle studies and monitoring. While the management of the data collection process was Internet-based, this additional eHealth communication channel was based on over-the-phone natural language conversation with a dialogue system utilizing automated speech recognition technology. For this study we implemented a dialogue system for patients' assessment and monitoring of chronic pain. METHODS: Experimental evaluation of usability of the Pain Monitoring Voice Diary was performed with 24 volunteers. The volunteers were asked to contribute 10 sessions with the system over a period of 2 weeks; in practice, the number of sessions per subject ranged from 1 to 20. The subjects were asked to either relate to pain episodes in their past while answering the system's questions, or use as a guidance one of nine provided medical scenarios compiled by a pain specialist, ranging from migraines and back pain to post-surgical pain (knee injury) and cancer- and chemotherapy-related afflictions. RESULTS: From 24 volunteers, we collected a total of 177 dialogue sessions: 171 sessions were completed, while the caller hung up in the other 6 sessions. There were a total of 2437 dialogue turns, where a dialogue turn corresponds to one system prompt and one user utterance. The data capture rate, measuring the percentage of slots filled automatically, was 98%, while the other 2% were flagged for transcription. Among the utterances sent to transcription, where the user had opted for the "none of those" option, 70% corresponded to the "type of pain" slot, 20% to the "symptoms" slot, and 10% to the "body part" slot, indicating that those are the grammars with the highest out-of-vocabulary rate. CONCLUSIONS: The results of this feasibility study indicated that desired accuracy of data can be achieved with a high degree of automation (98% in the study) and that the users were indeed capable of utilizing the flexible interface, the sessions becoming more and more efficient as users' experience increased, both in terms of session duration and avoidance of troublesome dialogue situations. [Abstract/Link to Full Text]

El Emam K, Jabbouri S, Sams S, Drouet Y, Power M
Evaluating common de-identification heuristics for personal health information.
J Med Internet Res. 2006;8(4):e28.
BACKGROUND: With the growing adoption of electronic medical records, there are increasing demands for the use of this electronic clinical data in observational research. A frequent ethics board requirement for such secondary use of personal health information in observational research is that the data be de-identified. De-identification heuristics are provided in the Health Insurance Portability and Accountability Act Privacy Rule, funding agency and professional association privacy guidelines, and common practice. OBJECTIVE: The aim of the study was to evaluate whether the re-identification risks due to record linkage are sufficiently low when following common de-identification heuristics and whether the risk is stable across sample sizes and data sets. METHODS: Two methods were followed to construct identification data sets. Re-identification attacks were simulated on these. For each data set we varied the sample size down to 30 individuals, and for each sample size evaluated the risk of re-identification for all combinations of quasi-identifiers. The combinations of quasi-identifiers that were low risk more than 50% of the time were considered stable. RESULTS: The identification data sets we were able to construct were the list of all physicians and the list of all lawyers registered in Ontario, using 1% sampling fractions. The quasi-identifiers of region, gender, and year of birth were found to be low risk more than 50% of the time across both data sets. The combination of gender and region was also found to be low risk more than 50% of the time. We were not able to create an identification data set for the whole population. CONCLUSIONS: Existing Canadian federal and provincial privacy laws help explain why it is difficult to create an identification data set for the whole population. That such examples of high re-identification risk exist for mainstream professions makes a strong case for not disclosing the high-risk variables and their combinations identified here. For professional subpopulations with published membership lists, many variables often needed by researchers would have to be excluded or generalized to ensure consistently low re-identification risk. Data custodians and researchers need to consider other statistical disclosure techniques for protecting privacy. [Abstract/Link to Full Text]

Norman CD, Skinner HA
eHEALS: The eHealth Literacy Scale.
J Med Internet Res. 2006;8(4):e27.
BACKGROUND: Electronic health resources are helpful only when people are able to use them, yet there remain few tools available to assess consumers' capacity for engaging in eHealth. Over 40% of US and Canadian adults have low basic literacy levels, suggesting that eHealth resources are likely to be inaccessible to large segments of the population. Using information technology for health requires eHealth literacy-the ability to read, use computers, search for information, understand health information, and put it into context. The eHealth Literacy Scale (eHEALS) was designed (1) to assess consumers' perceived skills at using information technology for health and (2) to aid in determining the fit between eHealth programs and consumers. OBJECTIVES: The eHEALS is an 8-item measure of eHealth literacy developed to measure consumers' combined knowledge, comfort, and perceived skills at finding, evaluating, and applying electronic health information to health problems. The objective of the study was to psychometrically evaluate the properties of the eHEALS within a population context. A youth population was chosen as the focus for the initial development primarily because they have high levels of eHealth use and familiarity with information technology tools. METHODS: Data were collected at baseline, post-intervention, and 3- and 6-month follow-up using control group data as part of a single session, randomized intervention trial evaluating Web-based eHealth programs. Scale reliability was tested using item analysis for internal consistency (coefficient alpha) and test-retest reliability estimates. Principal components factor analysis was used to determine the theoretical fit of the measures with the data. RESULTS: A total of 664 participants (370 boys; 294 girls) aged 13 to 21 (mean = 14.95; SD = 1.24) completed the eHEALS at four time points over 6 months. Item analysis was performed on the 8-item scale at baseline, producing a tight fitting scale with alpha = .88. Item-scale correlations ranged from r = .51 to .76. Test-retest reliability showed modest stability over time from baseline to 6-month follow-up (r = .68 to .40). Principal components analysis produced a single factor solution (56% of variance). Factor loadings ranged from .60 to .84 among the 8 items. CONCLUSIONS: The eHEALS reliably and consistently captures the eHealth literacy concept in repeated administrations, showing promise as tool for assessing consumer comfort and skill in using information technology for health. Within a clinical environment, the eHEALS has the potential to serve as a means of identifying those who may or may not benefit from referrals to an eHealth intervention or resource. Further research needs to examine the applicability of the eHEALS to other populations and settings while exploring the relationship between eHealth literacy and health care outcomes. [Abstract/Link to Full Text]

Adler KG
Web portals in primary care: an evaluation of patient readiness and willingness to pay for online services.
J Med Internet Res. 2006;8(4):e26.
BACKGROUND: Online Web communication between physician and patient has been proposed by leading primary care organizations as a way to enhance physician-patient communication, but lack of payment for this service has acted as a significant barrier to implementation. OBJECTIVE: This study evaluates current patient readiness and willingness to pay for online services in a fairly typical urban family medicine practice. METHODS: All patients that visited the author for medical care during a one-month period in the spring of 2006 were anonymously surveyed with a one-page survey instrument that inquired about demographics, willingness to pay a small annual fee for online services, the greatest fee they were willing to pay, and their most desired service. RESULTS: A total of 346 patients out of 2380 active patients in the study practice (14.5%) were surveyed. The valid survey response rate was 95.1% (329/346.) Three quarters, or 75.4%, of patients had Internet access. The group with the highest access were 18- to 29-year-olds (97%), and the group with the least access were those 70 years and up (56%) (P < .001). Categorized by employment, students and employed patients had the best access at 92% and 87%, respectively, and retirees and disabled patients had the worst access at 66% and 42%, respectively (P < .001). Of all patients with Internet access, 74.6% (n = 185) were willing to pay a small annual fee for one or more of the following online services: viewing of parts of their medical record, messaging with their physician, medication refills, appointment requests, and billing inquiries. Willingness to pay did not vary significantly by age (P = .06). Of all respondents, regardless of Internet access, 47.1% (n = 155) were willing to pay US $10 or more per year, with the median amount being US $20. Of those with Internet access (n = 248), 60.1% (n = 149) were willing to pay US $10 or more per year, and 31% were willing to pay US $50 or more per year. The three most important services to patients with Internet access (n = 248), in order of importance, were emailing with their physician (34%), Internet viewing of their medical record (22%), and medication refills (11%) (P < .001). CONCLUSIONS: This study suggests that patients of all ages are currently ready and willing to pay a small annual fee for online services with their primary care physician's office. If 47.1% of a practice of 2500 patients each paid US $10 per year for online services, the annual revenue generated would be US $11775. Not only does this study support the economic feasibility of patient Web portals, but it suggests that online services could form a new line of revenue for primary care physicians. [Abstract/Link to Full Text]

Kastner M, Wilczynski NL, Walker-Dilks C, McKibbon KA, Haynes B
Age-specific search strategies for Medline.
J Med Internet Res. 2006;8(4):e25.
BACKGROUND: Many clinicians and researchers are interested in patients of a specific age (childhood, geriatrics, and so on). Searching for age-specific publications in large bibliographic databases such as Medline is problematic because of inconsistencies in indexing, overlapping age categories, and the spread of the relevant literature over many journals. To our knowledge, no empirically tested age-specific search strategies exist for Medline. OBJECTIVE: We sought to determine the retrieval characteristics of age-specific terms in Medline for identifying studies relevant for five clinical specialties: adult medicine, geriatric medicine, pediatric medicine, neonatal medicine, and obstetrics. METHODS: We compared age-specific search terms and phrases for the retrieval of citations in Medline with a manual hand search of the literature for 161 core health care journals. Six experienced research assistants who were trained and intensively calibrated read all issues of 161 journals for the publishing year 2000. In addition to classifying all articles for purpose and quality, study participants' ages were also recorded. Outcome measures were sensitivity, specificity, precision, and accuracy of single and combination search terms. RESULTS: When maximizing sensitivity, the best sensitivity and specificity achieved with combination terms were 98% and 81.2%, respectively, for pediatric medicine, 96.4% and 55.9% for geriatric medicine, 95.3% and 83.6% for neonatal medicine, 94.9% and 64.5% for adult medicine, and 82% and 97.1% for obstetrics. When specificity was maximized, all disciplines had an expected decrease in sensitivity and an increase in precision. Highest values for optimizing best sensitivity and specificity were achieved in neonatal medicine, 92.5% and 92.6%, respectively. CONCLUSION: Selected single terms and combinations of MeSH terms and textwords can reliably retrieve age-specific studies cited in Medline. [Abstract/Link to Full Text]

Potts HW
Is e-health progressing faster than e-health researchers?
J Med Internet Res. 2006;8(3):e24.
Formal Internet interventions exist in a broad context of diverse online health resources, which share elements in common like information, advice and peer support. However, most online health resources are not created by healthcare professionals. Internet interventions need to be designed to "compete" in that wider context. The democratization of production and distribution is central to the transformative effect of the Internet on society, yet potentially conflicts with healthcare's need for an evidence base and safe practice. This is a core challenge for healthcare on the Internet. [Abstract/Link to Full Text]

Ritterband LM, Andersson G, Christensen HM, Carlbring P, Cuijpers P
Directions for the International Society for Research on Internet Interventions (ISRII).
J Med Internet Res. 2006;8(3):e23.
In 2004, the International Society for Research on Internet Interventions (ISRII) was formed to encourage eHealth researchers to collaborate in their efforts to further the science behind developing, testing, and disseminating Web-based treatment programs. The group held its second meeting (April 2006) to clarify the Society's direction and identify key issues that need addressing in the field. These issues are identified and examined in the current paper. Given the success of using the Internet to treat a range of medical and mental health problems, and the growing need for better dissemination of health care, Internet interventions will almost certainly play a prominent role in global health. ISRII plans to provide the necessary venue to ensure the science driving this field is strong, enabling researchers to conduct the highest quality research and permitting meaningful conclusions from completed studies. [Abstract/Link to Full Text]

Ahmad F, Hudak PL, Bercovitz K, Hollenberg E, Levinson W
Are physicians ready for patients with Internet-based health information?
J Med Internet Res. 2006;8(3):e22.
BACKGROUND: An increasing number of patients bring Internet-based health information to medical consultations. However, little is known about how physicians experience, manage, and view these patients. OBJECTIVE: This study aimed to advance the understanding of the effects of incorporating Internet-based health information into routine medical consultations from physicians' perspectives, using a qualitative approach. METHODS: Six focus groups were conducted with 48 family physicians practising in Toronto. The data were analyzed using qualitative methods of content analysis and constant comparison, derived from grounded theory approach. RESULTS: Three overarching themes were identified: (1) perceived reactions of patients, (2) physician burden, and (3) physician interpretation and contextualization of information. Physicians in our study generally perceived Internet-based health information as problematic when introduced by patients during medical consultations. They believed that Internet information often generated patient misinformation, leading to confusion, distress, or an inclination towards detrimental self-diagnosis and/or self-treatment. Physicians felt these influences added a new interpretive role to their clinical responsibilities. Although most of the physicians felt obliged to carry out this new responsibility, the additional role was often unwelcome. Despite identifying various reactions of patients to Internet-based health information, physicians in our study were unprepared to handle these patients. CONCLUSION: Effective initiatives at the level of the health care system are needed. The potential of Internet-based health information to lead to better physician-patient communication and patient outcomes could be facilitated by promoting physician acknowledgment of increasing use of the Internet among patients and by developing patient management guidelines and incentives for physicians. [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]

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]

Ritterband LM, Thorndike F
Internet interventions or patient education web sites?
J Med Internet Res. 2006;8(3):e18; author reply e19. [Abstract/Link to Full Text]

Kerr C, Murray E, Stevenson F, Gore C, Nazareth I
Internet interventions for long-term conditions: patient and caregiver quality criteria.
J Med Internet Res. 2006;8(3):e13.
BACKGROUND: Interactive health communication applications (IHCAs) that combine high-quality health information with interactive components, such as self-assessment tools, behavior change support, peer support, or decision support, are likely to benefit people with long-term conditions. IHCAs are now largely Web-based and are becoming known as "Internet interventions." Although there are numerous professionally generated criteria to assess health-related websites, to date there has been scant exploration of patient-generated assessment criteria even though patients and professionals use different criteria for assessing the quality of traditional sources of health information. OBJECTIVE: We aimed to determine patients' and caregivers' requirements of IHCAs for long-term conditions as well as their criteria for assessing the quality of different programs. METHODS: This was a qualitative study with focus groups. Patients and caregivers managing long-term conditions used three (predominantly Web-based) IHCAs relevant to their condition and subsequently discussed the strengths and weaknesses of the different IHCAs in focus groups. Participants in any one focus group all shared the same long-term condition and viewed the same three IHCAs. Patient and caregiver criteria for IHCAs emerged from the data. RESULTS: There were 40 patients and caregivers who participated in 10 focus groups. Participants welcomed the potential of Internet interventions but felt that many were not achieving their full potential. Participants generated detailed and specific quality criteria relating to information content, presentation, interactivity, and trustworthiness, which can be used by developers and purchasers of Internet interventions. CONCLUSIONS: The user-generated quality criteria reported in this paper should help developers and purchasers provide Internet interventions that better meet user needs. [Abstract/Link to Full Text]

Cobb NK, Graham AL
Characterizing Internet searchers of smoking cessation information.
J Med Internet Res. 2006;8(3):e17.
BACKGROUND: The Internet is a viable channel to deliver evidence-based smoking cessation treatment that has the potential to make a large population impact on reducing smoking prevalence. There is high demand for smoking cessation information and support on the Internet. Approximately 7% (10.2 million) of adult American Internet users have searched for information on quitting smoking. Little is known about these individuals, their smoking status, what type of cessation services they are seeking on the Internet, or how frequently these searches for cessation information are conducted. OBJECTIVE: The primary goal of this study was to characterize individuals who search for smoking cessation information on the Internet to determine appropriate triage and treatment strategies. The secondary goal was to estimate the incidence of searches for cessation information using publicly available search engine data. METHODS: We recruited individuals who clicked on a link to a leading smoking cessation website (QuitNet) from within the results of a search engine query. Individuals were "intercepted" before seeing the QuitNet home page and were invited to participate in the study. Those accepting the invitation were routed to an online survey about demographics, smoking characteristics, preferences for specific cessation services, and Internet search patterns. To determine the generalizability of our sample, national datasets on search engine usage patterns, market share, and keyword rankings were examined. These datasets were then used to estimate the number of queries for smoking cessation information each year. RESULTS: During the 10-day study period, 2265 individuals were recruited and 29% (N = 655) responded. Of these, 59% were female and overall tended to be younger than the previously characterized general Internet population. Most (76%) respondents were current smokers; 17% had quit within the last 7 days, and 7% had quit more than 7 days ago. Slightly more than half of active smokers (53%) indicated that they were planning to quit in the next 30 days. Smokers were more likely to seek information on how to quit and on medications; former smokers were more interested in how to cope with withdrawal. All participants rated withdrawal information and individually tailored information as being more useful, while displaying little interest in telephone counseling, expert support, or peer support. Publicly available data from large search engines suggest that 4 million Americans search for resources on smoking cessation each year. CONCLUSIONS: This study adds to the limited data available on individuals who search for smoking cessation information on the Internet, supports the prior estimates of the size of the population, and indicates that these individuals are in appropriate stages for both active cessation interventions and aggressive relapse prevention efforts. Continued development and evaluation of online interventions is warranted, and organizations seeking to promote cessation should carefully evaluate the Internet as a possible modality for treatment and as a gateway to other traditional programs. [Abstract/Link to Full Text]

Embi PJ, Acharya P, McCuistion M, Kishman CP, Haag D, Marine S
Responding rapidly to FDA drug withdrawals: design and application of a new approach for a consumer health website.
J Med Internet Res. 2006;8(3):e16.
BACKGROUND: Information about drug withdrawals may not reach patients in a timely manner, and this could result in adverse events. Increasingly, the public turns to consumer health websites for health information, but such sites may not update their content for days or weeks following important events like Food and Drug Administration (FDA) drug withdrawal actions. There is no recognized standard for how quickly consumer health websites should respond to such events, and reports addressing this issue are lacking. OBJECTIVE: The objective of this study was to develop and implement an approach to enhance the efficiency with which a consumer health website (NetWellness.org) responds to FDA drug withdrawal actions. METHODS: Evaluation of the current approach used by NetWellness staff to update content affected by FDA action revealed a slow process driven by the goal of performing thorough and comprehensive review and editing. To achieve our desired goal of accurately updating affected content within 24 hours of FDA action, we developed a strategy that included rapid updating of affected Web pages with warning boxes and hyperlinks to the information about the withdrawal. With the next FDA withdrawal event, that of valdecoxib (Bextra) on April 7, 2005, we applied this new approach, observed the time and resource requirements, and monitored the rate at which consumers viewed the updated information to gauge its potential impact. RESULTS: Application of the new approach allowed one person to modify the affected Web pages in less than 1 hour and within 18 hours of the FDA announcement. Using the old strategy, response to a similar event, the withdrawal of rofecoxib (Vioxx) 6 months earlier, had taken over 3 weeks and the efforts of several personnel. Updated valdecoxib content received 188 hits within the first month and 4285 hits within 1 year. CONCLUSIONS: Rapid updating of a consumer health website's content in response to an FDA drug withdrawal event was easily accomplished by applying the approach described. This allowed consumers to view accurate information regarding the withdrawn drug much sooner than would otherwise have been the case. Given that consumers increasingly turn to websites for their health information, adoption of a rapid response standard for important health events like FDA drug withdrawals should be considered by the consumer health informatics community. [Abstract/Link to Full Text]

Danaher BG, Boles SM, Akers L, Gordon JS, Severson HH
Defining participant exposure measures in Web-based health behavior change programs.
J Med Internet Res. 2006;8(3):e15.
BACKGROUND: Published research on the use of Web-based behavior change programs is growing rapidly. One of the observations characterized as problematic in these studies is that participants often make relatively few website visits and spend only a brief time accessing the program. Properly structured websites permit the unobtrusive measurement of the ways in which participants access (are exposed to) program content. Research on participant exposure to Web-based programs is not merely of interest to technologists, but represents an important opportunity to better understand the broader theme of program engagement and to guide the development of more effective interventions. OBJECTIVES: The current paper seeks to provide working definitions and describe initial patterns of various measures of participant exposure to ChewFree.com, a large randomized controlled trial of a Web-based program for smokeless tobacco cessation. METHODS: We examined measures of participant exposure to either an Enhanced condition Web-based program (interactive, tailored, and rich-media program) or a Basic condition control website (static, text-based material). Specific measures focused on email prompting, participant visits (number, duration, and pattern of use over time), and Web page viewing (number of views, types of pages viewed, and Web forum postings). RESULTS: Participants in the ChewFree.com Enhanced condition made more visits and spent more time accessing their assigned website than did participants assigned to the Basic condition website. In addition, exposure data demonstrated that Basic condition users thoroughly accessed program content, indicating that the condition provided a meaningful, face-valid control to the Enhanced condition. CONCLUSIONS: We recommend that researchers conducting evaluations of Web-based interventions consider the collection and analysis of exposure measures in the broader context of program engagement in order to assess whether participants obtain sufficient exposure to relevant program content. [Abstract/Link to Full Text]

McClure JB, Greene SM, Wiese C, Johnson KE, Alexander G, Strecher V
Interest in an online smoking cessation program and effective recruitment strategies: results from Project Quit.
J Med Internet Res. 2006;8(3):e14.
BACKGROUND: The Internet is a promising venue for delivering smoking cessation treatment, either as a stand-alone program or as an adjunct to pharmacotherapy. However, there is little data to indicate what percent of smokers are interested in receiving online smoking cessation services or how best to recruit smokers to Internet-based programs. OBJECTIVE: Using a defined recruitment sample, this study aimed to identify the percentage of smokers who expressed interest in or enrolled in Project Quit, a tailored, online, cognitive-behavioral support program offered with adjunctive nicotine replacement therapy patches. In addition, we examined the effectiveness of several individual-level versus population-level recruitment strategies. METHODS: Members from two large health care organizations in the United States were invited to participate in Project Quit. Recruitment efforts included proactive invitation letters mailed to 34533 likely smokers and reactive population-level study advertisements targeted to all health plan members (> 560000 adults, including an estimated 98000 smokers across both health care organizations). RESULTS: An estimated 1.6% and 2.5% of adult smokers from each health care organization enrolled in Project Quit. Among likely smokers who received proactive study invitations, 7% visited the Project Quit website (n = 2260) and 4% (n = 1273) were eligible and enrolled. Response rates were similar across sites, despite using different sources to assemble the invitation mailing list. Proactive individual-level recruitment was more effective than other forms of recruitment, accounting for 69% of website visitors and 68% of enrollees. CONCLUSIONS: Smokers were interested in receiving online smoking cessation support, even though they had access to other forms of treatment through their health insurance. Uptake rates for this program were comparable to those seen when smokers are advised to quit and are referred to other forms of smoking cessation treatment. In this sample, proactive mailings were the best method for recruiting smokers to Project Quit. [Abstract/Link to Full Text]

Norman CD, Skinner HA
eHealth Literacy: Essential Skills for Consumer Health in a Networked World.
J Med Internet Res. 2006;8(2):e9.
Electronic health tools provide little value if the intended users lack the skills to effectively engage them. With nearly half the adult population in the United States and Canada having literacy levels below what is needed to fully engage in an information-rich society, the implications for using information technology to promote health and aid in health care, or for eHealth, are considerable. Engaging with eHealth requires a skill set, or literacy, of its own. The concept of eHealth literacy is introduced and defined as the ability to seek, find, understand, and appraise health information from electronic sources and apply the knowledge gained to addressing or solving a health problem. In this paper, a model of eHealth literacy is introduced, comprised of multiple literacy types, including an outline of a set of fundamental skills consumers require to derive direct benefits from eHealth. A profile of each literacy type with examples of the problems patient-clients might present is provided along with a resource list to aid health practitioners in supporting literacy improvement with their patient-clients across each domain. Facets of the model are illustrated through a set of clinical cases to demonstrate how health practitioners can address eHealth literacy issues in clinical or public health practice. Potential future applications of the model are discussed. [Abstract/Link to Full Text]

Eysenbach G
The open access advantage.
J Med Internet Res. 2006;8(2):e8.
A study published today in PLoS Biology provides robust evidence that open-access articles are more immediately recognized and cited than non-OA articles. This editorial provides some additional follow up data from the most recent analysis of the same cohort in April 2006, 17 to 21 months after publication. These data suggest that the citation gap between open access and non-open access papers continues to widen. I conclude with the observation that the "open access advantage" has at least three components: (1) a citation count advantage (as a metric for knowledge uptake within the scientific community), (2) an end user uptake advantage, and (3) a cross-discipline fertilization advantage. More research is needed, and JMIR is inviting research on all aspects of open access. As the advantages for publishing open access from a researchers' point of view become increasingly clear, questions around the sustainability of open access journals remain. This journal is a living example that "lean publishing" models can create successful open access journals. Open source tools which have been developed by the Public Knowledge Project at the University of British Columbia with contributions from the Epublishing & Open Access group at the Centre for Global eHealth Innovation in Toronto are an alternative to hosting journals on commercial open access publisher sites. [Abstract/Link to Full Text]

Garritty C, El Emam K
Who's using PDAs? Estimates of PDA use by health care providers: a systematic review of surveys.
J Med Internet Res. 2006;8(2):e7.
BACKGROUND: Personal digital assistants (PDAs) find many uses in health care. Knowing rates of collective PDA use among health care providers is an important guiding step to further understanding those health care contexts that are most suited to PDA use and whether PDAs provide improved health outcomes. OBJECTIVES: The objectives of this study were to estimate current and future PDA use among health care providers and to discuss possible implications of that use on choice of technology in clinical practice and research. METHODS: This study was a systematic review of PDA usage surveys. Surveys were identified as part of an ongoing systematic review on the use of handheld devices. Reports from eight databases covering both biomedical sciences and engineering (1993-2006) were screened against distinct eligibility criteria. Data from included surveys were extracted and verified in a standardized way and were assessed descriptively. RESULTS: We identified 23 relevant surveys, 15 of which were derived from peer-reviewed journals. This cohort of surveys was published between 2000 and 2005. Overall, since 1999, there is clear evidence of an increasing trend in PDA use. The current overall adoption rate for individual professional use ranges between 45% and 85%, indicating high but somewhat variable adoption, primarily among physicians. CONCLUSIONS: Younger physicians and residents and those working in large and hospital-based practices are more likely to use a PDA. The adoption rate is now at its highest rate of increase according to a commonly accepted diffusion of innovations model. A common problem with the evaluation of information technology is that use frequently precedes research. This is the case here, in which PDA adoption rates are already high and projections are for rapid growth in the short term. In general, it appears that professional PDA use in health care settings involves more administrative and organizational tasks than those related to patient care, perhaps signaling where the growth in adoption is most likely to occur. We conclude that physicians are likely accustomed to using a PDA, and, therefore, technology expertise will probably not be a barrier to implementing PDA applications. However, there is an urgent need to evaluate the effectiveness and efficiency of specific tasks using handheld technology to inform those developing and those using PDA applications. [Abstract/Link to Full Text]

Ivanitskaya L, O'Boyle I, Casey AM
Health information literacy and competencies of information age students: results from the interactive online Research Readiness Self-Assessment (RRSA).
J Med Internet Res. 2006;8(2):e6.
BACKGROUND: In an era of easy access to information, university students who will soon enter health professions need to develop their information competencies. The Research Readiness Self-Assessment (RRSA) is based on the Information Literacy Competency Standards for Higher Education, and it measures proficiency in obtaining health information, evaluating the quality of health information, and understanding plagiarism. OBJECTIVE: This study aimed to measure the proficiency of college-age health information consumers in finding and evaluating electronic health information; to assess their ability to discriminate between peer-reviewed scholarly resources and opinion pieces or sales pitches; and to examine the extent to which they are aware of their level of health information competency. METHODS: An interactive 56-item online assessment, the Research Readiness Self-Assessment (RRSA), was used to measure the health information competencies of university students. We invited 400 students to take part in the study, and 308 participated, giving a response rate of 77%. The RRSA included multiple-choice questions and problem-based exercises. Declarative and procedural knowledge were assessed in three domains: finding health information, evaluating health information, and understanding plagiarism. Actual performance was contrasted with self-reported skill level. Upon answering all questions, students received a results page that summarized their numerical results and displayed individually tailored feedback composed by an experienced librarian. RESULTS: Even though most students (89%) understood that a one-keyword search is likely to return too many documents, few students were able to narrow a search by using multiple search categories simultaneously or by employing Boolean operators. In addition, nearly half of the respondents had trouble discriminating between primary and secondary sources of information as well as between references to journal articles and other published documents. When presented with questionable websites on nonexistent nutritional supplements, only 50% of respondents were able to correctly identify the website with the most trustworthy features. Less than a quarter of study participants reached the correct conclusion that none of the websites made a good case for taking the nutritional supplements. Up to 45% of students were unsure if they needed to provide references for ideas expressed in paraphrased sentences or sentences whose structure they modified. Most respondents (84%) believed that their research skills were good, very good, or excellent. Students' self-perceptions of skill tended to increase with increasing level of education. Self-reported skills were weakly correlated with actual skill level, operationalized as the overall RRSA score (Cronbach alpha = .78 for 56 RRSA items). CONCLUSIONS: While the majority of students think that their research skills are good or excellent, many of them are unable to conduct advanced information searches, judge the trustworthiness of health-related websites and articles, and differentiate between various information sources. Students' self-reports may not be an accurate predictor of their actual health information competencies. [Abstract/Link to Full Text]

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

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

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

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

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

Recent Articles in BMC Bioinformatics

Li P, Zhang C, Perkins EJ, Gong P, Deng Y
Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks.
BMC Bioinformatics. 2007;8 Suppl 7S13.
BACKGROUND: The regulation of gene expression is achieved through gene regulatory networks (GRNs) in which collections of genes interact with one another and other substances in a cell. In order to understand the underlying function of organisms, it is necessary to study the behavior of genes in a gene regulatory network context. Several computational approaches are available for modeling gene regulatory networks with different datasets. In order to optimize modeling of GRN, these approaches must be compared and evaluated in terms of accuracy and efficiency. RESULTS: In this paper, two important computational approaches for modeling gene regulatory networks, probabilistic Boolean network methods and dynamic Bayesian network methods, are compared using a biological time-series dataset from the Drosophila Interaction Database to construct a Drosophila gene network. A subset of time points and gene samples from the whole dataset is used to evaluate the performance of these two approaches. CONCLUSION: The comparison indicates that both approaches had good performance in modeling the gene regulatory networks. The accuracy in terms of recall and precision can be improved if a smaller subset of genes is selected for inferring GRNs. The accuracy of both approaches is dependent upon the number of selected genes and time points of gene samples. In all tested cases, DBN identified more gene interactions and gave better recall than PBN. [Abstract/Link to Full Text]

Landry M, Winters-Hilt S
Analysis of nanopore detector measurements using Machine-Learning methods, with application to single-molecule kinetic analysis.
BMC Bioinformatics. 2007;8 Suppl 7S12.
BACKGROUND: A nanopore detector has a nanometer-scale trans-membrane channel across which a potential difference is established, resulting in an ionic current through the channel in the pA-nA range. A distinctive channel current blockade signal is created as individually "captured" DNA molecules interact with the channel and modulate the channel's ionic current. The nanopore detector is sensitive enough that nearly identical DNA molecules can be classified with very high accuracy using machine learning techniques such as Hidden Markov Models (HMMs) and Support Vector Machines (SVMs). RESULTS: A non-standard implementation of an HMM, emission inversion, is used for improved classification. Additional features are considered for the feature vector employed by the SVM for classification as well: The addition of a single feature representing spike density is shown to notably improve classification results. Another, much larger, feature set expansion was studied (2500 additional features instead of 1), deriving from including all the HMM's transition probabilities. The expanded features can introduce redundant, noisy information (as well as diagnostic information) into the current feature set, and thus degrade classification performance. A hybrid Adaptive Boosting approach was used for feature selection to alleviate this problem. CONCLUSION: The methods shown here, for more informed feature extraction, improve both classification and provide biologists and chemists with tools for obtaining a better understanding of the kinetic properties of molecules of interest. [Abstract/Link to Full Text]

Thomson K, Amin I, Morales E, Winters-Hilt S
Preliminary nanopore cheminformatics analysis of aptamer-target binding strength.
BMC Bioinformatics. 2007;8 Suppl 7S11.
BACKGROUND: Aptamers are nucleic acids selected for their ability to bind to molecules of interest and may provide the basis for a whole new class of medicines. If the aptamer is simply a dsDNA molecule with a ssDNA overhang (a "sticky" end) then the segment of ssDNA that complements that overhang provides a known binding target with binding strength adjustable according to length of overhang. RESULTS: Two bifunctional aptamers are examined using a nanopore detector. They are chosen to provide sensitive, highly modulated, blockade signals with their captured ends, while their un-captured regions are designed to have binding moieties for complementary ssDNA targets. The bifunctional aptamers are duplex DNA on their channel-captured portion, and single-stranded DNA on their portion with binding ability. For short ssDNA, the binding is merely to the complementary strand of DNA, which is what is studied here - for 5-base and 6-base overhangs. CONCLUSION: A preliminary statistical analysis using hidden Markov models (HMMs) indicates a clear change in the blockade pattern upon binding by the single captured aptamer. This is also consistent with the hypothesis that significant conformational changes occur during the annealing binding event. In further work the objective is to simply extend this ssDNA portion to be a well-studied approximately 80 base ssDNA aptamer, joined to the same bifunctional aptamer molecular platform. [Abstract/Link to Full Text]

Winters-Hilt S, Davis A, Amin I, Morales E
Nanopore current transduction analysis of protein binding to non-terminal and terminal DNA regions: analysis of transcription factor binding, retroviral DNA terminus dynamics, and retroviral integrase-DNA binding.
BMC Bioinformatics. 2007;8 Suppl 7S10.
BACKGROUND: Synthetic transcription factors (STFs) promise to offer a powerful new therapeutic against Cancer, AIDS, and genetic disease. Currently, 10% of drugs are of this type, including salicylate and tamoxifen. STFs that can appropriately target (and release) their transcription factor binding sites on native genomic DNA provide a means to directly influence cellular mRNA production. An effective mechanism for screening amongst transcription factor (TF) candidates would itself be highly valued, and such may be possible with nanopore cheminformatics methods. RESULTS: It is hypothesized that binding targets on channel-captured molecules, that are well away from the channel-captured region, can be monitored insofar as their binding status, or history, is concerned. The first set of experiments we perform to explore this "transduction" hypothesis involve non-terminal dsDNA binding to protein (DNA TATA box receptor binding to TBP), where we show new experimental results and application of a new cheminformatics data analysis method. In the second series of experiments to explore the transduction hypothesis we examine terminal (blunt-ended) dsDNA binding to protein. We show experimental results before and after introduction of HIV's DNA integrase to a solution of bifunctional "Y" shaped aptamers that have an HIV consensus terminus exposed for interaction. CONCLUSION: X-ray crystallographic studies have guided our understanding of DNA structure for almost a century. It is still difficult, however, to translate the sequence-directed curvature information obtained through these tools to actual systems found in solution. With a nanopore detector the sequence-dependent conformation kinetics of DNA, especially at the DNA terminus, can be studied in a new way while still in solution and on a single molecule basis. [Abstract/Link to Full Text]

Wilkins D, Gusev Y, Loganantharaj R, Bridges S, Winters-Hilt S, Wren JD
Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.
BMC Bioinformatics. 2007;8 Suppl 7S1. [Abstract/Link to Full Text]

Kim H, Park H, Drake BL
Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations.
BMC Bioinformatics. 2007;8 Suppl 9S6.
BACKGROUND: The construction of literature-based networks of gene-gene interactions is one of the most important applications of text mining in bioinformatics. Extracting potential gene relationships from the biomedical literature may be helpful in building biological hypotheses that can be explored further experimentally. Recently, latent semantic indexing based on the singular value decomposition (LSI/SVD) has been applied to gene retrieval. However, the determination of the number of factors k used in the reduced rank matrix is still an open problem. RESULTS: In this paper, we introduce a way to incorporate a priori knowledge of gene relationships into LSI/SVD to determine the number of factors. We also explore the utility of the non-negative matrix factorization (NMF) to extract unrecognized gene relationships from the biomedical literature by taking advantage of known gene relationships. A gene retrieval method based on NMF (GR/NMF) showed comparable performance with LSI/SVD. CONCLUSION: Using known gene relationships of a given gene, we can determine the number of factors used in the reduced rank matrix and retrieve unrecognized genes related with the given gene by LSI/SVD or GR/NMF. [Abstract/Link to Full Text]

Torii M, Hu ZZ, Song M, Wu CH, Liu H
A comparison study on algorithms of detecting long forms for short forms in biomedical text.
BMC Bioinformatics. 2007;8 Suppl 9S5.
MOTIVATION: With more and more research dedicated to literature mining in the biomedical domain, more and more systems are available for people to choose from when building literature mining applications. In this study, we focus on one specific kind of literature mining task, i.e., detecting definitions of acronyms, abbreviations, and symbols in biomedical text. We denote acronyms, abbreviations, and symbols as short forms (SFs) and their corresponding definitions as long forms (LFs). The study was designed to answer the following questions; i) how well a system performs in detecting LFs from novel text, ii) what the coverage is for various terminological knowledge bases in including SFs as synonyms of their LFs, and iii) how to combine results from various SF knowledge bases. METHOD: We evaluated the following three publicly available detection systems in detecting LFs for SFs: i) a handcrafted pattern/rule based system by Ao and Takagi, ALICE, ii) a machine learning system by Chang et al., and iii) a simple alignment-based program by Schwartz and Hearst. In addition, we investigated the conceptual coverage of two terminological knowledge bases: i) the UMLS (the Unified Medical Language System), and ii) the BioThesaurus (a thesaurus of names for all UniProt protein records). We also implemented a web interface that provides a virtual integration of various SF knowledge bases. RESULTS: We found that detection systems agree with each other on most cases, and the existing terminological knowledge bases have a good coverage of synonymous relationship for frequently defined LFs. The web interface allows people to detect SF definitions from text and to search several SF knowledge bases. AVAILABILITY: The web site is http://gauss.dbb.georgetown.edu/liblab/SFThesaurus. [Abstract/Link to Full Text]

Yoo I, Hu X, Song IY
A coherent graph-based semantic clustering and summarization approach for biomedical literature and a new summarization evaluation method.
BMC Bioinformatics. 2007;8 Suppl 9S4.
BACKGROUND: A huge amount of biomedical textual information has been produced and collected in MEDLINE for decades. In order to easily utilize biomedical information in the free text, document clustering and text summarization together are used as a solution for text information overload problem. In this paper, we introduce a coherent graph-based semantic clustering and summarization approach for biomedical literature. RESULTS: Our extensive experimental results show the approach shows 45% cluster quality improvement and 72% clustering reliability improvement, in terms of misclassification index, over Bisecting K-means as a leading document clustering approach. In addition, our approach provides concise but rich text summary in key concepts and sentences. CONCLUSION: Our coherent biomedical literature clustering and summarization approach that takes advantage of ontology-enriched graphical representations significantly improves the quality of document clusters and understandability of documents through summaries. [Abstract/Link to Full Text]

Srinivasan P, Qiu XY
GO for gene documents.
BMC Bioinformatics. 2007;8 Suppl 9S3.
BACKGROUND: Annotating genes and their products with Gene Ontology codes is an important area of research. One approach is to use the information available about these genes in the biomedical literature. The goal in this paper, based on this approach, is to develop automatic annotation methods that can supplement the expensive manual annotation processes currently in place. RESULTS: Using a set of Support Vector Machines (SVM) classifiers we were able to achieve Fscores of 0.49, 0.41 and 0.33 for codes of the molecular function, cellular component and biological process GO hierarchies respectively. We find that alternative term weighting strategies are not different from each other in performance and feature selection strategies reduce performance. The best thresholding strategy is one where a single threshold is picked for each hierarchy. Hierarchy level is important especially for molecular function and biological process. The cellular component hierarchy stands apart from the other two in many respects. This may be due to fundamental differences in link semantics. This research shows that it is possible to beneficially exploit the hierarchical structures by defining and testing a relaxed criteria for classification correctness. Finally it is possible to build classifiers for codes with very few associated documents but as expected a huge penalty is paid in performance. CONCLUSION: The GO annotation problem is complex. Several key observations have been made as for example about topic drift that may be important to consider in annotation strategies. [Abstract/Link to Full Text]

Lee D, Kim S, Kim Y
BioCAD: an information fusion platform for bio-network inference and analysis.
BMC Bioinformatics. 2007;8 Suppl 9S2.
BACKGROUND: As systems biology has begun to draw growing attention, bio-network inference and analysis have become more and more important. Though there have been many efforts for bio-network inference, they are still far from practical applications due to too many false inferences and lack of comprehensible interpretation in the biological viewpoints. In order for applying to real problems, they should provide effective inference, reliable validation, rational elucidation, and sufficient extensibility to incorporate various relevant information sources. RESULTS: We have been developing an information fusion software platform called BioCAD. It is utilizing both of local and global optimization for bio-network inference, text mining techniques for network validation and annotation, and Web services-based workflow techniques. In addition, it includes an effective technique to elucidate network edges by integrating various information sources. This paper presents the architecture of BioCAD and essential modules for bio-network inference and analysis. CONCLUSION: BioCAD provides a convenient infrastructure for network inference and network analysis. It automates series of users' processes by providing data preprocessing tools for various formats of data. It also helps inferring more accurate and reliable bio-networks by providing network inference tools which utilize information from distinct sources. And it can be used to analyze and validate the inferred bio-networks using information fusion tools. [Abstract/Link to Full Text]

Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu Z, Liu H, Smith B, Wu CH
Framework for a protein ontology.
BMC Bioinformatics. 2007;8 Suppl 9S1.
Biomedical ontologies are emerging as critical tools in genomic and proteomic research, where complex data in disparate resources need to be integrated. A number of ontologies describe properties that can be attributed to proteins. For example, protein functions are described by the Gene Ontology (GO) and human diseases by SNOMED CT or ICD10. There is, however, a gap in the current set of ontologies - one that describes the protein entities themselves and their relationships. We have designed the PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modifications). PRO will allow the specification of relationships between PRO, GO and other ontologies in the OBO Foundry. Here we describe the initial development of PRO, illustrated using human and mouse proteins involved in the transforming growth factor-beta and bone morphogenetic protein signaling pathways. [Abstract/Link to Full Text]

Tamura T, Akutsu T
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition.
BMC Bioinformatics. 2007 Nov 30;8(1):466.
ABSTRACT: BACKGROUND: Subcellular location prediction of proteins is an important and well-studied problem in bioinformatics. This is a problem of predicting which part in a cell a given protein is transported to, where an amino acid sequence of the protein is given as an input. This problem is becoming more important since information on subcellular location is helpful for annotation of proteins and genes and the number of complete genomes is rapidly increasing. Since existing predictors are based on various heuristics, it is important to develop a simple method with high prediction accuracies. RESULTS: In this paper, we propose a novel and general predicting method by combining techniques for sequence alignment and feature vectors based on amino acid composition. We implemented this method with support vector machines on plant data sets extracted from the TargetP database. Through fivefold cross validation tests, the obtained overall accuracies and average MCC were 0.9096 and 0.8655 respectively. We also applied our method to other datasets including that of WoLFPSORT. CONCLUSIONS: Although there is a predictor which uses the information of gene ontology and yields higher accuracy than ours, our accuracies are higher than existing predictors which use only sequence information. Since such information as gene ontology can be obtained only for known proteins, our predictor is considered to be useful for subcellular location prediction of newly-discovered proteins. Furthermore, the idea of combination of alignment and amino acid frequency is novel and general so that it may be applied to other problems in bioinformatics. Our method for plant is also implemented as a web-system and available on [http://sunflower.kuicr.kyoto-u.ac.jp/\verb+~+tamura/slpfa.html]. [Abstract/Link to Full Text]

Dereeper A, Argout X, Billot C, Rami JF, Ruiz M
SAT, a flexible and optimized Web application for SSR marker development.
BMC Bioinformatics. 2007 Nov 29;8(1):465.
ABSTRACT: BACKGROUND: Simple Sequence Repeats (SSRs), or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched for SSR sequences, followed by DNA sequencing. However, designing optimal SSR markers from bulk sequence data is a laborious and time-consuming process. RESULTS: SAT (SSR Analysis Tool) is a user-friendly Web application developed to minimize tedious manual operations and reduce errors. This tool facilitates the integration, analysis and display of sequence data from SSR-enriched libraries. SAT is designed to successively perform base calling and quality evaluation of chromatograms, eliminate cloning vector, adaptors and low quality sequences, detect chimera or partially digested sequences, search for SSR motifs, cluster and assemble the redundant sequences, and design SSR primer pairs. An additional virtual PCR step establishes primer specificity. Users may modify the different parameters of each step of the SAT analysis. Although certain steps are compulsory, such as SSR motifs search and sequence assembly, users do not have to run the entire pipeline, and they can choose selectively which steps to perform. A database allows users to store and query results, and to redo individual steps of the workflow. CONCLUSIONS: The SAT Web application is available at http://sat.cirad.fr/sat, and a standalone command-line version is also freely downloadable. Users must send an email to the SAT administrator (tropgene@cirad.fr) to request a login and password. [Abstract/Link to Full Text]

Engelen S, Tahi F
Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences.
BMC Bioinformatics. 2007 Nov 28;8(1):464.
ABSTRACT: BACKGROUND: The secondary structure of an RNA must be known before the relations between its structure and function can be determined. One way to predict the secondary structure of an RNA is to identify covarying residues that maintain the pairings (Watson-Crick, Wobble and non-canonical pairings). This "comparative approach" consists of identifying mutations from homologous sequence alignments. The sequences must covary enough for compensatory mutations to be revealed, but comparison is difficult if they are too different. Thus the choice of homologous sequences is critical. While many possible combinations of homologous sequences may be used for prediction, only a few will give good structure predictions. This can be due to poor quality alignment in stems or to the variability of certain sequences. This problem of sequence selection is currently unsolved. RESULTS: This paper describes an algorithm, SSCA, which measures the suitability of sequences for comparative approach. It is based on evolutionary models with structure constraints, particularly those on sequence variations and stem alignment. We propose three models, based on different constraints on sequence alignments. We show the results of the SSCA algorithm for predicting the secondary structure of several RNAs. SSCA enabled us to choose sets of homologous sequences that gave better predictions than arbitrarily chosen sets of homologous sequences. CONCLUSIONS: SSCA is an algorithm for selecting combinations of RNA homologous sequences suitable for secondary structure predictions with the comparative approach. [Abstract/Link to Full Text]

Kumar M, Gromiha MM, Raghava GP
Identification of DNA-binding proteins using support vector machines and evolutionary profiles.
BMC Bioinformatics. 2007 Nov 27;8(1):463.
ABSTRACT: BACKGROUND: Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation, as these proteins play a crucial role in gene-regulation. In this paper, we developed various SVM modules for predicting DNA-binding domains and proteins. All models were trained and tested on multiple datasets of non-redundant proteins. RESULTS: SVM models have been developed on DNAaset, which consists of 1153 DNA-binding and equal number of non DNA-binding proteins, and achieved the maximum accuracy of 72.42% and 71.59% using amino acid and dipeptide compositions, respectively. The performance of SVM model improved from 72.42% to 74.22%, when evolutionary information in form of PSSM profiles was used as input instead of amino acid composition. In addition, SVM models have been developed on DNAset, which consists of 146 DNA-binding and 250 non-binding chains/domains, and achieved the maximum accuracy of 79.80% and 86.62% using amino acid composition and PSSM profiles. The SVM models developed in this study perform better than existing methods on a blind dataset. CONCLUSIONS: A highly accurate method has been developed for predicting DNA-binding proteins using SVM and PSSM profiles. This is the first study in which evolutionary information in form of PSSM profiles has been used successfully for predicting DNA-binding proteins. A web-server DNAbinder has been developed for identifying DNA-binding proteins and domains from query amino acid sequences (http://www.imtech.res.in/raghava/dnabinder/). [Abstract/Link to Full Text]

Di Cara A, Garg A, De Micheli G, Xenarios I, Mendoza L
Dynamic simulation of regulatory networks using SQUAD.
BMC Bioinformatics. 2007 Nov 26;8(1):462.
ABSTRACT: BACKGROUND: The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. RESULTS: We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by eliciting receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. CONCLUSIONS: The simulation of regulatory networks aims at predicting the behavior of a whole system when subject to stimuli, such as drugs, or determine the role of specific components within the network. The predictions can then be used to interpret and/or drive laboratory experiments. SQUAD provides a user-friendly graphical interface, accessible to both computational and experimental biologists for the fast qualitative simulation of large regulatory networks for which kinetic data is not necessarily available. [Abstract/Link to Full Text]

Casneuf T, Van de Peer Y, Huber W
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation.
BMC Bioinformatics. 2007 Nov 26;8(1):461.
ABSTRACT: BACKGROUND: Microarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated signals can result from technical deficiencies like hybridization of reporters with off-target transcripts. An approach that is able to distinguish these factors permits the detection of more biologically relevant co-expression signatures. RESULTS: We demonstrate a positive relation between off-target reporter alignment strength and expression correlation in data from oligonucleotide genechips. Furthermore, we describe a method that allows the identification, from their expression data, of individual probe sets affected by off-target hybridization. CONCLUSIONS: The effects of off-target hybridization on expression correlation coefficients can be substantial, and can be alleviated by more accurate mapping between microarray reporters and the target transcriptome. We recommend attention to the mapping for any microarray analysis of gene expression patterns. [Abstract/Link to Full Text]

Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R
Dendroscope: An interactive viewer for large phylogenetic trees.
BMC Bioinformatics. 2007 Nov 22;8(1):460.
ABSTRACT: BACKGROUND: Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an efficient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are difficult to install or are not available for all common operating systems. RESULTS: We have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP. CONCLUSIONS: Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets. [Abstract/Link to Full Text]

Rajapakse M, Schmidt B, Feng L, Brusic V
Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms.
BMC Bioinformatics. 2007 Nov 22;8(1):459.
ABSTRACT: BACKGROUND: Peptides binding to Major Histocompatibility Complex (MHC) class II molecules are crucial for initiation and regulation of immune responses. Predicting peptides that bind to a specific MHC molecule plays an important role in determining potential candidates for vaccines. The binding groove in class II MHC is open at both ends, allowing peptides longer than 9-mer to bind. Finding the consensus motif facilitating the binding of peptides to a MHC class II molecule is difficult because of different lengths of binding peptides and varying location of 9-mer binding core. The level of difficulty increases when the molecule is promiscuous and binds to a large number of low affinity peptides. In this paper, we propose two approaches using multi-objective evolutionary algorithms (MOEA) for predicting peptides binding to MHC class II molecules. One uses the information from both binders and non-binders for self-discovery of motifs. The other, in addition, uses information from experimentally determined motifs for guided-discovery of motifs. RESULTS: The proposed methods are intended for finding peptides binding to MHC class II I-Ag7 molecule - a promiscuous binder to a large number of low affinity peptides. Cross-validation results across experiments on two motifs derived for I-Ag7 datasets demonstrate better generalization abilities and accuracies of the present method over earlier approaches. Further, the proposed method was validated and compared on two publicly available benchmark datasets: (1) an ensemble of qualitative HLA-DRB1*0401 peptide data obtained from five different sources, and (2) quantitative peptide data obtained for sixteen different alleles comprising of three mouse alleles and thirteen HLA alleles. The proposed method outperformed earlier methods on most datasets, indicating that it is well suited for finding peptides binding to MHC class II molecules. CONCLUSIONS: We present two MOEA-based algorithms for finding motifs, one for self-discovery and the other for guided-discovery by experimentally determined motifs, and thereby predicting binding peptides to I-Ag7 molecule. Our experiments show that the proposed MOEA-based algorithms are better than earlier methods in predicting binding sites not only on I-Ag7 but also on most alleles of class II MHC benchmark datasets. This shows that our methods could be applicable to find binding motifs in a wide range of alleles. [Abstract/Link to Full Text]

Arenas M, Posada D
Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography.
BMC Bioinformatics. 2007 Nov 20;8(1):458.
ABSTRACT: BACKGROUND: Coalescent simulations have proven very useful in many population genetics studies. In order to arrive to meaningful conclusions, it is important that these simulations resemble the process of molecular evolution as much as possible. To date, no single coalescent program is able to simulate codon sequences sampled from populations with recombination, migration and growth. RESULTS: We introduce a new coalescent program, called Recodon, which is able to simulate samples of coding DNA sequences under complex scenarios in which several evolutionary forces can interact simultaneously (namely, recombination, migration and demography). The basic codon model implemented is an extension to the general time-reversible model of nucleotide substitution with a proportion of invariable sites and among-site rate variation. In addition, the program implements non-reversible processes and mixtures of different codon models. CONCLUSIONS: Recodon is a flexible tool for the simulation of coding DNA sequences under realistic evolutionary models. These simulations can be used to build parameter distributions for testing evolutionary hypotheses using experimental data. Recodon is written in C, can run in parallel, and is freely available from http://darwin.uvigo.es/. [Abstract/Link to Full Text]

Fujita A, Sato JR, Ferreira CE, Sogayar MC
GEDI: a user-friendly toolbox for analysis of large-scale gene expression data.
BMC Bioinformatics. 2007 Nov 19;8(1):457.
ABSTRACT: BACKGROUND: Several mathematical and statistical methods have been proposed in the last few years to analyze microarray data. Most of those methods involve complicated formulas, and software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties when they attempting to use those methods in their research. Here we present an user-friendly toolbox which allows large-scale gene expression analysis to be carried out by biomedical researchers with limited programming skills. RESULTS: Here, we introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source, and freely-available tool that we believe will be useful to a wide range of laboratories, and to researchers with no background in Mathematics and Computer Science, allowing them to analyze their own data by applying both classical and advanced approaches developed and recently published by Fujita et al. CONCLUSIONS: GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us. It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations. Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology. [Abstract/Link to Full Text]

Bare JC, Shannon PT, Schmid AK, Baliga NS
The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.
BMC Bioinformatics. 2007 Nov 19;8(1):456.
ABSTRACT: BACKGROUND: Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. RESULTS: The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. CONCLUSIONS: The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools. [Abstract/Link to Full Text]

Pin C, Reuter M
Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA - a Bayesian approach.
BMC Bioinformatics. 2007 Nov 19;8(1):455.
ABSTRACT: BACKGROUND: Microarrays are widely used for the study of gene expression; however deciding on whether observed differences in expression are significant remains a challenge. RESULTS: A computing tool (ArrayLeaRNA) has been developed for gene expression analysis. It implements a Bayesian approach which is based on the Gumbel distribution and uses printed genomic DNA control features for normalization and for estimation of the parameters of the Bayesian model and prior knowledge from predicted operon structure. The method is compared with two other approaches: the classical LOWESS normalization followed by a two fold cut-off criterion and the OpWise method (Price, et al. 2006. BMC Bioinformatics. 7, 19), a published Bayesian approach also using predicted operon structure The three methods were compared on experimental datasets with prior knowledge of gene expression. With ArrayLeaRNA, data normalization is carried out according to the genomic features which reflect the results of equally transcribed genes; also the statistical significance of the difference in expression is based on the variability of the equally transcribed genes. The operon information helps the classification of genes with low confidence measurements. ArrayLeaRNA is implemented in Visual Basic and freely available as an Excel add-in at http://www.ifr.ac.uk/safety/ArrayLeaRNA/ CONCLUSIONS: We have introduced a novel Bayesian model and demonstrated that it is a robust method for analysing microarray expression profiles. ArrayLeaRNA showed a considerable improvement in data normalization, in the estimation of the experimental variability intrinsic to each hybridization and in the establishment of a clear boundary between non-changing and differentially expressed genes. The method is applicable to data derived from hybridizations of labelled cDNA samples as well as from hybridizations of labelled cDNA with genomic DNA and can be used for the analysis of datasets where differentially regulated genes predominate. [Abstract/Link to Full Text]

Redestig H, Weicht D, Selbig J, Hannah MA
Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana.
BMC Bioinformatics. 2007 Nov 18;8(1):454.
ABSTRACT: BACKGROUND: The central role of transcription factors (TFs) in higher eukaryotes has led to much interest in deciphering transcriptional regulatory interactions. Even in the best case, experimental identification of TF target genes is error prone, and has been shown to be improved by considering additional forms of evidence such as expression data. Previous expression based methods have not explicitly tried to associate TFs with their targets and therefore largely ignored the treatment specific and time dependent nature of transcription regulation. RESULTS: In this study we introduce CERMT, Covariance based Extraction of Regulatory targets using Multiple Time series. Using simulated and real data we show that using multiple expression time series, selecting treatments in which the TF responds, allowing time shifts between TFs and their targets and using covariance to identify highly responding genes appear to be a good strategy. We applied our method to published TF - target gene relationships determined using expression profiling on TF mutants and show that in most cases we obtain significant target gene enrichment and in half of the cases this is sufficient to deliver a usable list of high-confidence target genes. CONCLUSIONS: CERMT could be immediately useful in refining possible target genes of candidate TFs using publicly available data, particularly for organisms lacking comprehensive TF binding data. In the future, we believe its incorporation with other forms of evidence may improve integrative genome-wide predictions of transcriptional networks. [Abstract/Link to Full Text]

Kim TM, Chung YJ, Rhyu MG, Jung MH
Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis.
BMC Bioinformatics. 2007 Nov 17;8(1):453.
ABSTRACT: BACKGROUND: Gene clustering has been widely used to group genes with similar expression pattern in microarray data analysis. Subsequent enrichment analysis using predefined gene sets can provide clues on which functional themes or regulatory sequence motifs are associated with individual gene clusters. In spite of the potential utility, gene clustering and enrichment analysis have been used in separate platforms, thus, the development of integrative algorithm linking both methods is highly challenging. RESULTS: In this study, we propose an algorithm for discovery of molecular functions and elucidation of transcriptional logics using two kinds of gene information, functional and regulatory motif gene sets. The algorithm, termed gene set expression coherence analysis first selects functional gene sets with significantly high expression coherences. Those candidate gene sets are further processed into a number of functionally related themes or functional clusters according to the expression similarities. Each functional cluster is then, investigated for the enrichment of transcriptional regulatory motifs using modified gene set enrichment analysis and regulatory motif gene sets. The method was tested for two publicly available expression profiles representing murine myogenesis and erythropoiesis. For respective profiles, our algorithm identified myocyte- and erythrocyte-related molecular functions, along with the putative transcriptional regulators for the corresponding molecular functions. CONCLUSION: As an integrative and comprehensive method for the analysis of large-scaled gene expression profiles, our method is able to generate a set of testable hypotheses: the transcriptional regulator X regulates function Y under cellular condition Z. GSECA algorithm is implemented into standalone software package, which is freely available at http://www.systemsbiology.co.kr/GSECA/. [Abstract/Link to Full Text]

Cheng C, Yan X, Sun F, Li LM
Inferring activity changes of transcription factors by binding association with sorted expression profiles.
BMC Bioinformatics. 2007 Nov 16;8(1):452.
ABSTRACT: BACKGROUND: The identification of transcription factors (TFs) associated with a biological process is fundamental to understanding its regulatory mechanisms. From microarray data, however, the activity changes of TFs often cannot be directly observed due to their relatively low expression levels, post-transcriptional modifications, and other complications. Several approaches have been proposed to infer TF activity changes from microarray data. In some models, a linear relationship between gene expression and TF-gene binding strength is assumed. In some other models, the target genes of a TF are first determined by a significance cutoff to binding affinity scores, and then expression differentiation is checked between the target and other genes. RESULTS: We propose a novel method, referred to as BASE (binding association with sorted expression), to infer TF activity changes from microarray expression profiles with the help of binding affinity data. It searches the maximum association between bind affinity profile of a TF and expression change profile along the direction of sorted differentiation. The method does not make hard target gene selection, rather, the significances of TF activity changes are evaluated by permutation tests of binding association at the end. To show the effectiveness of this method, we apply it to three typical examples using different kinds of binding affinity data, namely, ChIP-chip data, motif discovery data, and positional weighted matrix scanning data, respectively. The implications obtained from all three examples are consistent with established biological results. Moreover, the inferences suggest new and biologically meaningful hypotheses for further investigation. CONCLUSIONS: The proposed method makes transcription inference from profiles of expression and binding affinity. The same machinery can be used to deal with various kinds of binding affinity data. The method does not require a linear assumption, and has the desirable property of scale-invariance with respect to TF-specific binding affinity. This method is easy to implement and can be routinely applied for transcriptional inferences in microarray studies. [Abstract/Link to Full Text]

Abe K, Kobayashi N, Sode K, Ikebukuro K
Peptide ligand screening of alpha-synuclein aggregation modulators by in silico panning.
BMC Bioinformatics. 2007 Nov 16;8(1):451.
ABSTRACT: BACKGROUND: alpha-Synuclein is a Parkinson's-disease-related protein. It forms aggregates in vivo, and these aggregates cause cell cytotoxicity. Aggregation inhibitors are expected to reduce alpha-synuclein cytotoxicity, and an aggregation accelerator has recently been reported to reduce alpha-synuclein cytotoxicity. Therefore, amyloid aggregation modulating ligands are expected to serve as therapeutic medicines. RESULTS: We screened peptide ligands against alpha-synuclein by in silico panning, a method which we have proposed previously. In this study, we selected as the target a very hydrophobic region known as the amyloid-core-forming region. Since this region cannot be dissolved in water, it is difficult to carry out the in vitro screening of its peptide ligand. We carried out 6 rounds of in silico panning using a genetic algorithm and a docking simulation. After the in silico panning, we evaluated the top peptides screened in silico by in vitro assay. These peptides were capable of binding to alpha-synuclein. CONCLUSIONS: We demonstrated that it is possible to screen alpha-synuclein-binding peptides by in silico panning. The screened peptides bind to alpha-synuclein, thus affecting the aggregation of alpha-synuclein. [Abstract/Link to Full Text]

Tian J, Wu N, Guo X, Guo J, Zhang J, Fan Y
Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines.
BMC Bioinformatics. 2007 Nov 16;8(1):450.
ABSTRACT: BACKGROUND: Human genetic variations primarily result from single nucleotide polymorphisms (SNPs) that occur approximately every 1000 bases in the overall human population. The non-synonymous SNPs (nsSNPs) that lead to amino acid changes in the protein product may account for nearly half of the known genetic variations linked to inherited human diseases. One of the key problems of medical genetics today is to identify nsSNPs that underlie disease-related phenotypes in humans. As such, the development of computational tools that can identify such nsSNPs would enhance our understanding of genetic diseases and help predict the disease. RESULTS: We propose a method, named Parepro (Predicting the amino acid replacement probability), to identify nsSNPs having either deleterious or neutral effects on the resulting protein function. Two independent datasets, HumVar and NewHumVar, taken from the PhD-SNP server, were applied to train the model and test the robustness of Parepro. Using a 20-fold cross validation test on the HumVar dataset, Parepro achieved a Matthews correlation coefficient (MCC) of 50% and an overall accuracy (Q2) of 76%, both of which were higher than those predicted by the methods, such as PolyPhen, SIFT, and HydridMeth. Further analysis on an additional dataset (NewHumVar) using Parepro yielded similar results. CONCLUSIONS: The performance of Parepro indicates that it is a powerful tool for predicting the effect of nsSNPs on protein function and would be useful for large-scale analysis of genomic nsSNP data. [Abstract/Link to Full Text]

Robinson MD, Speed TP
A comparison of Affymetrix gene expression arrays.
BMC Bioinformatics. 2007 Nov 15;8(1):449.
ABSTRACT: BACKGROUND: Affymetrix GeneChipsTM are an important tool in many facets of biological research. Recently, notable design changes to the chips have been made. In this study, we use publicly available data from Affymetrix to gauge the performance of three human gene expression arrays: Human Genome U133 Plus 2.0 (U133), Human Exon 1.0 ST (HuEx) and Human Gene 1.0 ST (HuGene). RESULTS: We studied probe-, exon- and gene-level reproducibility of technical and biological replicates from each of the 3 platforms. The U133 array has larger feature sizes so it is no surprise that probe-level variances are smaller, however the larger number of probes per gene on the HuGene array seems to produce gene-level summaries that have similar variances. The gene-level summaries of the HuEx array are less reproducible than the other two, despite having the largest average number of probes per gene. Greater than 80% of the content on the HuEx arrays is expressed at or near background. Biological variation seems to have a smaller effect on U133 data. Comparing the overlap of differentially expressed genes, we see a high overall concordance among all 3 platforms, with HuEx and HuGene having greater overlap, as expected given their design. We performed an analysis of detection rates and area under ROC curves using an experiment made up of several mixtures of 2 human tissues. Though it appears that the HuEx array has worse performance in terms of detection rates, all arrays have similar ability to separate differentially expressed and non-differentially expressed genes. CONCLUSIONS: Despite noticeable differences in the probe-level reproducibility, gene-level reproducibility and differential expression detection are quite similar across the three platforms. The HuEx array, an all-encompassing array, has the flexibility of measuring all known or predicted exonic content. However, the HuEx array induces poorer reproducibility for genes with fewer exons. The HuGene measures just the well-annotated genome content and appears to perform well. The U133 array, though not able to measure across the full length of a transcript, appears to perform as well as the newer designs on the set of genes common to all 3 platforms. [Abstract/Link to Full Text]

Curtin K, Wong J, Allen-Brady K, Camp NJ
PedGenie: meta genetic association testing in mixed family and case-control designs.
BMC Bioinformatics. 2007 Nov 15;8(1):448.
ABSTRACT: BACKGROUND: PedGenie software, introduced in 2006, includes genetic association testing of cases and controls that may be independent or related (nuclear families or extended pedigrees) or mixtures thereof using Monte Carlo significance testing. Our aim is to demonstrate that PedGenie, a unique and flexible analysis tool freely available in Genie 2.4 software, is significantly enhanced by incorporating meta statistics for detecting genetic association with disease using data across multiple study groups. METHODS: Meta statistics (chi-squared tests, odds ratios, and confidence intervals) were calculated using formal Cochran-Mantel-Haenszel techniques. Simulated data from unrelated individuals and individuals in families were used to illustrate meta tests and their empirically-derived p-values and confidence intervals are accurate, precise, and for independent designs match those provided by standard statistical software. RESULTS: PedGenie yields accurate Monte Carlo p-values for meta analysis of data across multiple studies, based on validation testing using pedigree, nuclear family, and case-control data simulated under both the null and alternative hypotheses of a genotype-phenotype association. CONCLUSIONS: PedGenie allows valid combined analysis of data from mixtures of pedigree-based and case-control resources. Added meta capabilities provide new avenues for association analysis, including pedigree resources from large consortia and multi-center studies. [Abstract/Link to Full Text]

Recent Articles in Biomedical Digital Libraries

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Recent Articles in Cell Biology Education

Campbell AM
Meeting report: synthetic biology Jamboree for undergraduates.
Cell Biol Educ. 2005;4(1):19-23. [Abstract/Link to Full Text]

Watters C
Video views and reviews: cytokinesis: a phenomenon overlooked too often.
Cell Biol Educ. 2005;4(1):10-8. [Abstract/Link to Full Text]

Labov JB
From the National Academies: medical school admissions requirements and undergraduate science education.
Cell Biol Educ. 2005;4(1):7-9. [Abstract/Link to Full Text]

Allen D, Tanner K
Approaches to biology teaching and learning: from a scholarly approach to teaching to the scholarship of teaching.
Cell Biol Educ. 2005;4(1):1-6. [Abstract/Link to Full Text]

Lopatto D
Survey of Undergraduate Research Experiences (SURE): first findings.
Cell Biol Educ. 2004;3(4):270-7.
In this study, I examined the hypothesis that undergraduate research enhances the educational experience of science undergraduates, attracts and retains talented students to careers in science, and acts as a pathway for minority students into science careers. Undergraduates from 41 institutions participated in an online survey on the benefits of undergraduate research experiences. Participants indicated gains on 20 potential benefits and reported on career plans. Over 83% of 1,135 participants began or continued to plan for postgraduate education in the sciences. A group of 51 students who discontinued their plans for postgraduate science education reported significantly lower gains than continuing students. Women and men reported similar levels of benefits and similar patterns of career plans. Ethnic groups did not significantly differ in reported levels of benefits or plans to continue with postgraduate education. [Abstract/Link to Full Text]

Gibbons NJ, Evans C, Payne A, Shah K, Griffin DK
Computer simulations improve university instructional laboratories.
Cell Biol Educ. 2004;3(4):263-9.
Laboratory classes are commonplace and essential in biology departments but can sometimes be cumbersome, unreliable, and a drain on time and resources. As university intakes increase, pressure on budgets and staff time can often lead to reduction in practical class provision. Frequently, the ability to use laboratory equipment, mix solutions, and manipulate test animals are essential learning outcomes, and "wet" laboratory classes are thus appropriate. In others, however, interpretation and manipulation of the data are the primary learning outcomes, and here, computer-based simulations can provide a cheaper, easier, and less time- and labor-intensive alternative. We report the evaluation of two computer-based simulations of practical exercises: the first in chromosome analysis, the second in bioinformatics. Simulations can provide significant time savings to students (by a factor of four in our first case study) without affecting learning, as measured by performance in assessment. Moreover, under certain circumstances, performance can be improved by the use of simulations (by 7% in our second case study). We concluded that the introduction of these simulations can significantly enhance student learning where consideration of the learning outcomes indicates that it might be appropriate. In addition, they can offer significant benefits to teaching staff. [Abstract/Link to Full Text]

Tomanek D, Montplaisir L
Students' studying and approaches to learning in introductory biology.
Cell Biol Educ. 2004;3(4):253-62.
This exploratory study was conducted in an introductory biology course to determine 1) how students used the large lecture environment to create their own learning tasks during studying and 2) whether meaningful learning resulted from the students' efforts. Academic task research from the K-12 education literature and student approaches to learning research from the postsecondary education literature provided the theoretical framework for the mixed methods study. The subject topic was cell division. Findings showed that students 1) valued lectures to develop what they believed to be their own understanding of the topic; 2) deliberately created and engaged in learning tasks for themselves only in preparation for the unit exam; 3) used course resources, cognitive operations, and study strategies that were compatible with surface and strategic, rather than deep, approaches to learning; 4) successfully demonstrated competence in answering familiar test questions aligned with their surface and strategic approaches to studying and learning; and 5) demonstrated limited meaningful understanding of the significance of cell division processes. Implications for introductory biology education are discussed. [Abstract/Link to Full Text]

Rice M, Gladstone W, Weir M
Relational databases: a transparent framework for encouraging biology students to think informatically.
Cell Biol Educ. 2004;3(4):241-52.
We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills. [Abstract/Link to Full Text]

Silva TD, da Cunha Aguiar LC, Leta J, Santos DO, Cardoso FS, Cabral LM, Rodrigues CR, Castro HC
Role of the undergraduate student research assistant in the new millennium.
Cell Biol Educ. 2004;3(4):235-40.
In this study, we analyze the contribution of the undergraduate student who participates in the process of generating scientific data and developing a research project using Brazilian research as an example. Historically, undergraduate students have performed the critical role of research assistants in developing countries. This aspect has been underappreciated as a means of generating scientific data in Brazilian research facilities. Brazilian educational institutions are facing major age-related generational changes among the science faculty within the next 5-10 yr. A lack of adequate support for graduate students leads to a concern that undergraduates will not be interested in choosing research assistant programs and, subsequently, academic research careers. To remedy this situation it is important to focus on ways to encourage new research careers and enhance university-industry collaborations. [Abstract/Link to Full Text]

Blystone RV
WWW.Cell Biology Education.
Cell Biol Educ. 2004;3(4):223-7. [Abstract/Link to Full Text]

Watters C
Video views and reviews: creating a thread with respect to the invasion of animal viruses.
Cell Biol Educ. 2004;3(4):218-22. [Abstract/Link to Full Text]

Wood WB, Handelsman J
Meeting report: the 2004 National Academies Summer Institute on Undergraduate Education in Biology.
Cell Biol Educ. 2004;3(4):215-7. [Abstract/Link to Full Text]

Labov JB
From the National Academies: the challenges and opportunities for improving undergraduate science education through introductory courses.
Cell Biol Educ. 2004;3(4):212-4. [Abstract/Link to Full Text]

Lodish HF, Rodriguez RK, Klionsky DJ
Points of view: lectures: can't learn with them, can't learn without them.
Cell Biol Educ. 2004;3(4):202-11. [Abstract/Link to Full Text]

Tanner K, Allen D
Approaches to biology teaching and learning: learning styles and the problem of instructional selection--engaging all students in science courses.
Cell Biol Educ. 2004;3(4):197-201. [Abstract/Link to Full Text]

Felix DA, Hertle MD, Conley JG, Washington LB, Bruns PJ
Assessing precollege science education outreach initiatives: a funder's perspective.
Cell Biol Educ. 2004;3(3):189-95.
We describe an assessment of the collective impact of 35 grants that the Howard Hughes Medical Institute (HHMI) made to biomedical research institutions in 1999 to support precollege science education outreach programs. Data collected from funded institutions were compared with data from a control group of institutions that had advanced to the last stage of review but had not been funded. The survey instrument and the results reveal outcomes and impacts that HHMI considers relevant for these programs. The following attributes are considered: ability to secure additional, non-HHMI funding; institution buy-in as measured by gains in dedicated space and staff; enhancement of the program director's career; number and adoption of educational products developed; number of related publications and awards; percentage of programs for which teachers received course credit; increase in science content knowledge; and increase in student motivation to study science. [Abstract/Link to Full Text]

Stith BJ
Use of animation in teaching cell biology.
Cell Biol Educ. 2004;3(3):181-8.
To address the different learning styles of students, and because students can access animation from off-campus computers, the use of digital animation in teaching cell biology has become increasingly popular. Sample processes from cell biology that are more clearly presented in animation than in static illustrations are identified. The value of animation is evaluated on whether the process being taught involves motion, cellular location, or sequential order of numerous events. Computer programs for developing animation and animations associated with cell biology textbooks are reviewed, and links to specific examples of animation are given. Finally, future teaching tools for all fields of biology will increasingly benefit from an expansion of animation to the use of simulation. One purpose of this review is to encourage the widespread use of animations in biology teaching by discussing the nature of digital animation. [Abstract/Link to Full Text]

Niemann MA, Miller ML, Davis T
The University of Alabama at Birmingham Center for Community OutReach Development Summer Science Institute Program: a 3-yr laboratory research experience for inner-city secondary-level students.
Cell Biol Educ. 2004;3(3):162-80.
This article describes and assesses the effectiveness of a 3-yr, laboratory-based summer science program to improve the academic performance of inner-city high school students. The program was designed to gradually introduce such students to increasingly more rigorous laboratory experiences in an attempt to interest them in and model what "real" science is like. The students are also exposed to scientific seminars and university tours as well as English and mathematics workshops designed to help them analyze their laboratory data and prepare for their closing ceremony presentations. Qualitative and quantitative analysis of student performance in these programs indicates that participants not only learn the vocabulary, facts, and concepts of science, but also develop a better appreciation of what it is like to be a "real" scientist. In addition, the college-bound 3-yr graduates of this program appear to be better prepared to successfully academically compete with graduates of other high schools; they also report learning useful job-related life skills. Finally, the critical conceptual components of this program are discussed so that science educators interested in using this model can modify it to fit the individual resources and strengths of their particular setting. [Abstract/Link to Full Text]

PowerPoint in the classroom.
Cell Biol Educ. 2004;3(3):155-61.
Points of View (POV) addresses issues faced within life science education. Cell Biology Education has launched the POV feature to present two or more opinions published in tandem on a common topic. We consider POVs to be "Op-Ed" pieces designed to stimulate thought and dialog on significant educational issues. Each author has the opportunity to revise a POV after reading drafts of the other POVs. In this issue, we ask the question, "Is PowerPoint the best instructional medium to use in your class?" Everyone seems to have an opinion on Microsoft, but the intellectual merits of using PowerPoint (or similar software) is a growing question as states and institutions put more and more money into information technology and distance learning. Four POVs are presented: 1) David Keefe and James Willett provide their case why PowerPoint is an ideal teaching software. Keefe is an educational researcher at the Center for Technology in Learning at SRI International. Willett is a professor at George Mason University in the Departments of Microbial and Molecular Bioscience; as well as Bioinformatics and Computational Biology. 2) Kim McDonald highlights the causes of PowerPointlessness, a term which indicates the frequent use of PowerPoint as a crutch rather than a tool. She is a Bioscience Educator at the Shodor Education Foundation, Inc. 3) Diana Voss asks readers if PowerPoint is really necessary to present the material effectively or not. Voss is a Instructional Computing Support Specialist at SUNY Stony Brook. 4) Cynthia Lanius takes a light-hearted approach to ask whether PowerPoint is a technological improvement or just a change of pace for teacher and student presentations. Lanius is a Technology Integration Specialist in the Sinton (Texas) Independent School District. The authors span the range of teaching experiences and settings from which they bring different points of view to the debate. Readers are encouraged to participate in the online discussion forum hosted by CBE at www.cellbioed.org/discussion/public/main.cfm and/or contact the authors directly. [Abstract/Link to Full Text]

Wenzel TJ
Outcomes from the undergraduate research summit.
Cell Biol Educ. 2004;3(3):150-1. [Abstract/Link to Full Text]

Ricks I
The 50th Anniversary of Brown v. Board of Education: continued impacts on minority life science education.
Cell Biol Educ. 2004;3(3):146-9. [Abstract/Link to Full Text]

Watters C
Video views and reviews: Golgi export, targeting, and plasma membrane caveolae.
Cell Biol Educ. 2004;3(3):141-5. [Abstract/Link to Full Text]

Arwood L
Teaching cell biology to nonscience majors through forensics, or how to design a killer course.
Cell Biol Educ. 2004;3(2):131-8.
Nonscience majors often do not respond to traditional lecture-only biology courses. However, these students still need exposure to basic biological concepts. To accomplish this goal, forensic science was paired with compatible cell biology subjects. Several topics such as human development and molecular biology were found to fulfill this purpose. Another goal was to maximize the hands-on experience of the nonscience major students. This objective was fulfilled by specific activities such as fingerprinting and DNA typing. One particularly effective teaching tool was a mock murder mystery complete with a Grand Jury trial. Another objective was to improve students' attitudes toward science. This was successful in that students felt more confident in their own scientific abilities after taking the course. In pre/post tests, students answered four questions about their ability to conduct science. All four statements showed a positive shift after the course (p values ranging from.001 to.036, df = 23; n = 24). The emphasis on experiential pedagogy was also shown to increase critical thinking skills. In pre/post testing, students in this course significantly increased their performance on critical thinking assessment tests from 33.3% correct to 45.3% (p =.008, df = 4; n = 24). [Abstract/Link to Full Text]

Moreno NP, Denk JP, Roberts JK, Tharp BZ, Bost M, Thomson WA
An approach to improving science knowledge about energy balance and nutrition among elementary- and middle-school students.
Cell Biol Educ. 2004;3(2):122-30.
Unhealthy diets, lack of fitness, and obesity are serious problems in the United States. The Centers for Disease Control, Surgeon General, and Department of Health and Human Services are calling for action to address these problems. Scientists and educators at Baylor College of Medicine and the National Space Biomedical Research Institute teamed to produce an instructional unit, "Food and Fitness," and evaluated it with students in grades 3-7 in Houston, Texas. A field-test group (447 students) completed all unit activities under the guidance of their teachers. This group and a comparison group (343 students) completed pre and postassessments measuring knowledge of concepts covered in the unit. Outcomes indicate that the unit significantly increased students' knowledge and awareness of science concepts related to energy in living systems, metabolism, nutrients, and diet. Pre-assessment results suggest that most students understand concepts related to calories in food, exercise and energy use, and matching food intake to energy use. Students' prior knowledge was found to be much lower on topics related to healthy portion sizes, foods that supply the most energy, essential nutrients, what "diet" actually means, and the relationship between body size and basal metabolic rate. [Abstract/Link to Full Text]

Khodor J, Halme DG, Walker GC
A hierarchical biology concept framework: a tool for course design.
Cell Biol Educ. 2004;3(2):111-21.
A typical undergraduate biology curriculum covers a very large number of concepts and details. We describe the development of a Biology Concept Framework (BCF) as a possible way to organize this material to enhance teaching and learning. Our BCF is hierarchical, places details in context, nests related concepts, and articulates concepts that are inherently obvious to experts but often difficult for novices to grasp. Our BCF is also cross-referenced, highlighting interconnections between concepts. We have found our BCF to be a versatile tool for design, evaluation, and revision of course goals and materials. There has been a call for creating Biology Concept Inventories, multiple-choice exams that test important biology concepts, analogous to those in physics, astronomy, and chemistry. We argue that the community of researchers and educators must first reach consensus about not only what concepts are important to test, but also how the concepts should be organized and how that organization might influence teaching and learning. We think that our BCF can serve as a catalyst for community-wide discussion on organizing the vast number of concepts in biology, as a model for others to formulate their own BCFs and as a contribution toward the creation of a comprehensive BCF. [Abstract/Link to Full Text]

Ara�jo-Jorge TC, Cardona TS, Mendes CL, Henriques-Pons A, Meirelles RM, Coutinho CM, Aguiar LE, Meirelles Mde N, de Castro SL, Barbosa HS, Luz MR
Microscopy images as interactive tools in cell modeling and cell biology education.
Cell Biol Educ. 2004;3(2):99-110.
The advent of genomics, proteomics, and microarray technology has brought much excitement to science, both in teaching and in learning. The public is eager to know about the processes of life. In the present context of the explosive growth of scientific information, a major challenge of modern cell biology is to popularize basic concepts of structures and functions of living cells, to introduce people to the scientific method, to stimulate inquiry, and to analyze and synthesize concepts and paradigms. In this essay we present our experience in mixing science and education in Brazil. For two decades we have developed activities for the science education of teachers and undergraduate students, using microscopy images generated by our work as cell biologists. We describe open-air outreach education activities, games, cell modeling, and other practical and innovative activities presented in public squares and favelas. Especially in developing countries, science education is important, since it may lead to an improvement in quality of life while advancing understanding of traditional scientific ideas. We show that teaching and research can be mutually beneficial rather than competing pursuits in advancing these goals. [Abstract/Link to Full Text]

Heyden RJ
Approaches to cell biology: developing educational multimedia.
Cell Biol Educ. 2004;3(2):93-8. [Abstract/Link to Full Text]

Hoy R
New math for biology is the old new math.
Cell Biol Educ. 2004;3(2):90-2. [Abstract/Link to Full Text]

Brent R
Intuition and innumeracy.
Cell Biol Educ. 2004;3(2):88-90. [Abstract/Link to Full Text]

Gross LJ
Interdisciplinarity and the undergraduate biology curriculum: finding a balance.
Cell Biol Educ. 2004;3(2):85-7. [Abstract/Link to Full Text]

Recent Articles in BMC Medical Informatics and Decision Making

Dahl R, Gyrd-Hansen D, Kristiansen IS, Nex�e J, Bo Nielsen J
Can postponement of an adverse outcome be used to present risk reductions to a lay audience? A population survey.
BMC Med Inform Decis Mak. 2007;78.
BACKGROUND: For shared decision making doctors need to communicate the effectiveness of therapies such that patients can understand it and discriminate between small and large effects. Previous research indicates that patients have difficulties in understanding risk measures. This study aimed to test the hypothesis that lay people may be able to discriminate between therapies when their effectiveness is expressed in terms of postponement of an adverse disease event. METHODS: In 2004 a random sample of 1,367 non-institutionalized Danes aged 40+ was interviewed in person. The participants were asked for demographic information and asked to consider a hypothetical preventive drug treatment. The respondents were randomized to the magnitude of treatment effectiveness (heart attack postponement of 1 month, 6 months, 12 months, 2 years, 4 years and 8 years) and subsequently asked whether they would take such a therapy. They were also asked whether they had hypercholesterolemia or had experienced a heart attack. RESULTS: In total 58% of the respondents consented to the hypothetical treatment. The proportions accepting treatment were 39%, 52%, 56%, 64%, 67% and 73% when postponement was 1 month, 6 months, 12 months, 2 years, 4 years and 8 years respectively. Participants who thought that the effectiveness information was difficult to understand, were less likely to consent to therapy (p = 0.004). CONCLUSION: Lay people can discriminate between levels of treatment effectiveness when they are presented in terms of postponement of an adverse event. The results indicate that such postponement is a comprehensible measure of effectiveness. [Abstract/Link to Full Text]

Clauson KA, Marsh WA, Polen HH, Seamon MJ, Ortiz BI
Clinical decision support tools: analysis of online drug information databases.
BMC Med Inform Decis Mak. 2007;77.
BACKGROUND: Online drug information databases are used to assist in enhancing clinical decision support. However, the choice of which online database to consult, purchase or subscribe to is likely made based on subjective elements such as history of use, familiarity, or availability during professional training. The purpose of this study was to evaluate clinical decision support tools for drug information by systematically comparing the most commonly used online drug information databases. METHODS: Five commercially available and two freely available online drug information databases were evaluated according to scope (presence or absence of answer), completeness (the comprehensiveness of the answers), and ease of use. Additionally, a composite score integrating all three criteria was utilized. Fifteen weighted categories comprised of 158 questions were used to conduct the analysis. Descriptive statistics and Chi-square were used to summarize the evaluation components and make comparisons between databases. Scheffe's multiple comparison procedure was used to determine statistically different scope and completeness scores. The composite score was subjected to sensitivity analysis to investigate the effect of the choice of percentages for scope and completeness. RESULTS: The rankings for the databases from highest to lowest, based on composite scores were Clinical Pharmacology, Micromedex, Lexi-Comp Online, Facts & Comparisons 4.0, Epocrates Online Premium, RxList.com, and Epocrates Online Free. Differences in scope produced three statistical groupings with Group 1 (best) performers being: Clinical Pharmacology, Micromedex, Facts & Comparisons 4.0, Lexi-Comp Online, Group 2: Epocrates Premium and RxList.com and Group 3: Epocrates Free (p < 0.05). Completeness scores were similarly stratified. Collapsing the databases into two groups by access (subscription or free), showed the subscription databases performed better than the free databases in the measured criteria (p < 0.001). CONCLUSION: Online drug information databases, which belong to clinical decision support, vary in their ability to answer questions across a range of categories. [Abstract/Link to Full Text]

Jackson ML, Baer A, Painter I, Duchin J
A simulation study comparing aberration detection algorithms for syndromic surveillance.
BMC Med Inform Decis Mak. 2007;76.
BACKGROUND: The usefulness of syndromic surveillance for early outbreak detection depends in part on effective statistical aberration detection. However, few published studies have compared different detection algorithms on identical data. In the largest simulation study conducted to date, we compared the performance of six aberration detection algorithms on simulated outbreaks superimposed on authentic syndromic surveillance data. METHODS: We compared three control-chart-based statistics, two exponential weighted moving averages, and a generalized linear model. We simulated 310 unique outbreak signals, and added these to actual daily counts of four syndromes monitored by Public Health--Seattle and King County's syndromic surveillance system. We compared the sensitivity of the six algorithms at detecting these simulated outbreaks at a fixed alert rate of 0.01. RESULTS: Stratified by baseline or by outbreak distribution, duration, or size, the generalized linear model was more sensitive than the other algorithms and detected 54% (95% CI = 52%-56%) of the simulated epidemics when run at an alert rate of 0.01. However, all of the algorithms had poor sensitivity, particularly for outbreaks that did not begin with a surge of cases. CONCLUSION: When tested on county-level data aggregated across age groups, these algorithms often did not perform well in detecting signals other than large, rapid increases in case counts relative to baseline levels. [Abstract/Link to Full Text]

Le�n SA, Fontelo P, Green L, Ackerman M, Liu F
Evidence-based medicine among internal medicine residents in a community hospital program using smart phones.
BMC Med Inform Decis Mak. 2007;75.
BACKGROUND: This study implemented and evaluated a point-of-care, wireless Internet access using smart phones for information retrieval during daily clinical rounds and academic activities of internal medicine residents in a community hospital. We did the project to assess the feasibility of using smart phones as an alternative to reach online medical resources because we were unable to find previous studies of this type. In addition, we wanted to learn what Web-based information resources internal medicine residents were using and whether providing bedside, real-time access to medical information would be perceived useful for patient care and academic activities. METHODS: We equipped the medical teams in the hospital wards with smart phones (mobile phone/PDA hybrid devices) to provide immediate access to evidence-based resources developed at the National Library of Medicine as well as to other medical Websites. The emphasis of this project was to measure the convenience and feasibility of real-time access to current medical literature using smart phones. RESULTS: The smart phones provided real-time mobile access to medical literature during daily rounds and clinical activities in the hospital. Physicians found these devices easy to use. A post-study survey showed that the information retrieved was perceived to be useful for patient care and academic activities. CONCLUSION: In community hospitals and ambulatory clinics without wireless networks where the majority of physicians work, real-time access to current medical literature may be achieved through smart phones. Immediate availability of reliable and updated information obtained from authoritative sources on the Web makes evidence-based practice in a community hospital a reality. [Abstract/Link to Full Text]

Watkins RE, Eagleson S, Beckett S, Garner G, Veenendaal B, Wright G, Plant AJ
Using GIS to create synthetic disease outbreaks.
BMC Med Inform Decis Mak. 2007;74.
BACKGROUND: The ability to detect disease outbreaks in their early stages is a key component of efficient disease control and prevention. With the increased availability of electronic health-care data and spatio-temporal analysis techniques, there is great potential to develop algorithms to enable more effective disease surveillance. However, to ensure that the algorithms are effective they need to be evaluated. The objective of this research was to develop a transparent user-friendly method to simulate spatial-temporal disease outbreak data for outbreak detection algorithm evaluation. A state-transition model which simulates disease outbreaks in daily time steps using specified disease-specific parameters was developed to model the spread of infectious diseases transmitted by person-to-person contact. The software was developed using the MapBasic programming language for the MapInfo Professional geographic information system environment. RESULTS: The simulation model developed is a generalised and flexible model which utilises the underlying distribution of the population and incorporates patterns of disease spread that can be customised to represent a range of infectious diseases and geographic locations. This model provides a means to explore the ability of outbreak detection algorithms to detect a variety of events across a large number of stochastic replications where the influence of uncertainty can be controlled. The software also allows historical data which is free from known outbreaks to be combined with simulated outbreak data to produce files for algorithm performance assessment. CONCLUSION: This simulation model provides a flexible method to generate data which may be useful for the evaluation and comparison of outbreak detection algorithm performance. [Abstract/Link to Full Text]

Tolentino HD, Matters MD, Walop W, Law B, Tong W, Liu F, Fontelo P, Kohl K, Payne DC
A UMLS-based spell checker for natural language processing in vaccine safety.
BMC Med Inform Decis Mak. 2007;73.
BACKGROUND: The Institute of Medicine has identified patient safety as a key goal for health care in the United States. Detecting vaccine adverse events is an important public health activity that contributes to patient safety. Reports about adverse events following immunization (AEFI) from surveillance systems contain free-text components that can be analyzed using natural language processing. To extract Unified Medical Language System (UMLS) concepts from free text and classify AEFI reports based on concepts they contain, we first needed to clean the text by expanding abbreviations and shortcuts and correcting spelling errors. Our objective in this paper was to create a UMLS-based spelling error correction tool as a first step in the natural language processing (NLP) pipeline for AEFI reports. METHODS: We developed spell checking algorithms using open source tools. We used de-identified AEFI surveillance reports to create free-text data sets for analysis. After expansion of abbreviated clinical terms and shortcuts, we performed spelling correction in four steps: (1) error detection, (2) word list generation, (3) word list disambiguation and (4) error correction. We then measured the performance of the resulting spell checker by comparing it to manual correction. RESULTS: We used 12,056 words to train the spell checker and tested its performance on 8,131 words. During testing, sensitivity, specificity, and positive predictive value (PPV) for the spell checker were 74% (95% CI: 74-75), 100% (95% CI: 100-100), and 47% (95% CI: 46%-48%), respectively. CONCLUSION: We created a prototype spell checker that can be used to process AEFI reports. We used the UMLS Specialist Lexicon as the primary source of dictionary terms and the WordNet lexicon as a secondary source. We used the UMLS as a domain-specific source of dictionary terms to compare potentially misspelled words in the corpus. The prototype sensitivity was comparable to currently available tools, but the specificity was much superior. The slow processing speed may be improved by trimming it down to the most useful component algorithms. Other investigators may find the methods we developed useful for cleaning text using lexicons specific to their area of interest. [Abstract/Link to Full Text]

Kaner E, Heaven B, Rapley T, Murtagh M, Graham R, Thomson R, May C
Medical communication and technology: a video-based process study of the use of decision aids in primary care consultations.
BMC Med Inform Decis Mak. 2007;72.
BACKGROUND: Much of the research on decision-making in health care has focused on consultation outcomes. Less is known about the process by which clinicians and patients come to a treatment decision. This study aimed to quantitatively describe the behaviour shown by doctors and patients during primary care consultations when three types of decision aids were used to promote treatment decision-making in a randomised controlled trial. METHODS: A video-based study set in an efficacy trial which compared the use of paper-based guidelines (control) with two forms of computer-based decision aids (implicit and explicit versions of DARTS II). Treatment decision concerned warfarin anti-coagulation to reduce the risk of stroke in older patients with atrial fibrillation. Twenty nine consultations were video-recorded. A ten-minute 'slice' of the consultation was sampled for detailed content analysis using existing interaction analysis protocols for verbal behaviour and ethological techniques for non-verbal behaviour. RESULTS: Median consultation times (quartiles) differed significantly depending on the technology used. Paper-based guidelines took 21 (19-26) minutes to work through compared to 31 (16-41) minutes for the implicit tool; and 44 (39-55) minutes for the explicit tool. In the ten minutes immediately preceding the decision point, GPs dominated the conversation, accounting for 64% (58-66%) of all utterances and this trend was similar across all three arms of the trial. Information-giving was the most frequent activity for both GPs and patients, although GPs did this at twice the rate compared to patients and at higher rates in consultations involving computerised decision aids. GPs' language was highly technically focused and just 7% of their conversation was socio-emotional in content; this was half the socio-emotional content shown by patients (15%). However, frequent head nodding and a close mirroring in the direction of eye-gaze suggested that both parties were active participants in the conversation CONCLUSION: Irrespective of the arm of the trial, both patients' and GPs' behaviour showed that they were reciprocally engaged in these consultations. However, even in consultations aimed at promoting shared decision-making, GPs' were verbally dominant, and they worked primarily as information providers for patients. In addition, computer-based decision aids significantly prolonged the consultations, particularly the later phases. These data suggest that decision aids may not lead to more 'sharing' in treatment decision-making and that, in their current form, they may take too long to negotiate for use in routine primary care. [Abstract/Link to Full Text]

Siadaty MS, Shu J, Knaus WA
Relemed: sentence-level search engine with relevance score for the MEDLINE database of biomedical articles.
BMC Med Inform Decis Mak. 2007;71.
BACKGROUND: Receiving extraneous articles in response to a query submitted to MEDLINE/PubMed is common. When submitting a multi-word query (which is the majority of queries submitted), the presence of all query words within each article may be a necessary condition for retrieving relevant articles, but not sufficient. Ideally a relationship between the query words in the article is also required. We propose that if two words occur within an article, the probability that a relation between them is explained is higher when the words occur within adjacent sentences versus remote sentences. Therefore, sentence-level concurrence can be used as a surrogate for existence of the relationship between the words.In order to avoid the irrelevant articles, one solution would be to increase the search specificity. Another solution is to estimate a relevance score to sort the retrieved articles. However among the >30 retrieval services available for MEDLINE, only a few estimate a relevance score, and none detects and incorporates the relation between the query words as part of the relevance score. RESULTS: We have developed "Relemed", a search engine for MEDLINE. Relemed increases specificity and precision of retrieval by searching for query words within sentences rather than the whole article. It uses sentence-level concurrence as a statistical surrogate for the existence of relationship between the words. It also estimates a relevance score and sorts the results on this basis, thus shifting irrelevant articles lower down the list.In two case studies, we demonstrate that the most relevant articles appear at the top of the Relemed results, while this is not necessarily the case with a PubMed search. We have also shown that a Relemed search includes not only all the articles retrieved by PubMed, but potentially additional relevant articles, due to the extended 'automatic term mapping' and text-word searching features implemented in Relemed. CONCLUSION: By using sentence-level matching, Relemed can deliver higher specificity, thus eliminating more false-positive articles. By introducing an appropriate relevance metric, the most relevant articles on which the user wishes to focus are listed first. Relemed also shrinks the displayed text, and hence the time spent scanning the articles. [Abstract/Link to Full Text]

Boissy P, Jacobs K, Roy SH
Usability of a barcode scanning system as a means of data entry on a PDA for self-report health outcome questionnaires: a pilot study in individuals over 60 years of age.
BMC Med Inform Decis Mak. 2006;642.
BACKGROUND: Throughout the medical and paramedical professions, self-report health status questionnaires are used to gather patient-reported outcome measures. The objective of this pilot study was to evaluate in individuals over 60 years of age the usability of a PDA-based barcode scanning system with a text-to-speech synthesizer to collect data electronically from self-report health outcome questionnaires. METHODS: Usability of the system was tested on a sample of 24 community-living older adults (7 men, 17 women) ranging in age from 63 to 93 years. After receiving a brief demonstration on the use of the barcode scanner, participants were randomly assigned to complete two sets of 16 questions using the bar code wand scanner for one set and a pen for the other. Usability was assessed using directed interviews with a usability questionnaire and performance-based metrics (task times, errors, sources of errors). RESULTS: Overall, participants found barcode scanning easy to learn, easy to use, and pleasant. Participants were marginally faster in completing the 16 survey questions when using pen entry (20/24 participants). The mean response time with the barcode scanner was 31 seconds longer than traditional pen entry for a subset of 16 questions (p = 0.001). The responsiveness of the scanning system, expressed as first scan success rate, was less than perfect, with approximately one-third of first scans requiring a rescan to successfully capture the data entry. The responsiveness of the system can be explained by a combination of factors such as the location of the scanning errors, the type of barcode used as an answer field in the paper version, and the optical characteristics of the barcode scanner. CONCLUSION: The results presented in this study offer insights regarding the feasibility, usability and effectiveness of using a barcode scanner with older adults as an electronic data entry method on a PDA. While participants in this study found their experience with the barcode scanning system enjoyable and learned to become proficient in its use, the responsiveness of the system constitutes a barrier to wide-scale use of such a system. Optimizing the graphical presentation of the information on paper should significantly increase the system's responsiveness. [Abstract/Link to Full Text]

Tsuruta H, Bax L
Polychotomization of continuous variables in regression models based on the overall C index.
BMC Med Inform Decis Mak. 2006;641.
BACKGROUND: When developing multivariable regression models for diagnosis or prognosis, continuous independent variables can be categorized to make a prediction table instead of a prediction formula. Although many methods have been proposed to dichotomize prognostic variables, to date there has been no integrated method for polychotomization. The latter is necessary when dichotomization results in too much loss of information or when central values refer to normal states and more dispersed values refer to less preferable states, a situation that is not unusual in medical settings (e.g. body temperature, blood pressure). The goal of our study was to develop a theoretical and practical method for polychotomization. METHODS: We used the overall discrimination index C, introduced by Harrel, as a measure of the predictive ability of an independent regressor variable and derived a method for polychotomization mathematically. Since the na�ve application of our method, like some existing methods, gives rise to positive bias, we developed a parametric method that minimizes this bias and assessed its performance by the use of Monte Carlo simulation. RESULTS: The overall C is closely related to the area under the ROC curve and the produced di(poly)chotomized variable's predictive performance is comparable to the original continuous variable. The simulation shows that the parametric method is essentially unbiased for both the estimates of performance and the cutoff points. Application of our method to the predictor variables of a previous study on rhabdomyolysis shows that it can be used to make probability profile tables that are applicable to the diagnosis or prognosis of individual patient status. CONCLUSION: We propose a polychotomization (including dichotomization) method for independent continuous variables in regression models based on the overall discrimination index C and clarified its meaning mathematically. To avoid positive bias in application, we have proposed and evaluated a parametric method. The proposed method for polychotomizing continuous regressor variables performed well and can be used to create probability profile tables. [Abstract/Link to Full Text]

Burr T, Graves T, Klamann R, Michalak S, Picard R, Hengartner N
Accounting for seasonal patterns in syndromic surveillance data for outbreak detection.
BMC Med Inform Decis Mak. 2006;640.
BACKGROUND: Syndromic surveillance (SS) can potentially contribute to outbreak detection capability by providing timely, novel data sources. One SS challenge is that some syndrome counts vary with season in a manner that is not identical from year to year.Our goal is to evaluate the impact of inconsistent seasonal effects on performance assessments (false and true positive rates) in the context of detecting anomalous counts in data that exhibit seasonal variation. METHODS: To evaluate the impact of inconsistent seasonal effects, we injected synthetic outbreaks into real data and into data simulated from each of two models fit to the same real data. Using real respiratory syndrome counts collected in an emergency department from 2/1/94-5/31/03, we varied the length of training data from one to eight years, applied a sequential test to the forecast errors arising from each of eight forecasting methods, and evaluated their detection probabilities (DP) on the basis of 1000 injected synthetic outbreaks. We did the same for each of two corresponding simulated data sets. The less realistic, nonhierarchical model's simulated data set assumed that "one season fits all," meaning that each year's seasonal peak has the same onset, duration, and magnitude. The more realistic simulated data set used a hierarchical model to capture violation of the "one season fits all" assumption. RESULTS: This experiment demonstrated optimistic bias in DP estimates for some of the methods when data simulated from the nonhierarchical model was used for DP estimation, thus suggesting that at least for some real data sets and methods, it is not adequate to assume that "one season fits all." CONCLUSION: For the data we analyze, the "one season fits all " assumption is violated, and DP performance claims based on simulated data that assume "one season fits all," for the forecast methods considered, except for moving average methods, tend to be optimistic. Moving average methods based on relatively short amounts of training data are competitive on all three data sets, but are particularly competitive on the real data and on data from the hierarchical model, which are the two data sets that violate the "one season fits all" assumption. [Abstract/Link to Full Text]

Pomi A, Olivera F
Context-sensitive autoassociative memories as expert systems in medical diagnosis.
BMC Med Inform Decis Mak. 2006;639.
BACKGROUND: The complexity of our contemporary medical practice has impelled the development of different decision-support aids based on artificial intelligence and neural networks. Distributed associative memories are neural network models that fit perfectly well to the vision of cognition emerging from current neurosciences. METHODS: We present the context-dependent autoassociative memory model. The sets of diseases and symptoms are mapped onto a pair of basis of orthogonal vectors. A matrix memory stores the associations between the signs and symptoms, and their corresponding diseases. A minimal numerical example is presented to show how to instruct the memory and how the system works. In order to provide a quick appreciation of the validity of the model and its potential clinical relevance we implemented an application with real data. A memory was trained with published data of neonates with suspected late-onset sepsis in a neonatal intensive care unit (NICU). A set of personal clinical observations was used as a test set to evaluate the capacity of the model to discriminate between septic and non-septic neonates on the basis of clinical and laboratory findings. RESULTS: We show here that matrix memory models with associations modulated by context can perform automatic medical diagnosis. The sequential availability of new information over time makes the system progress in a narrowing process that reduces the range of diagnostic possibilities. At each step the system provides a probabilistic map of the different possible diagnoses to that moment. The system can incorporate the clinical experience, building in that way a representative database of historical data that captures geo-demographical differences between patient populations. The trained model succeeds in diagnosing late-onset sepsis within the test set of infants in the NICU: sensitivity 100%; specificity 80%; percentage of true positives 91%; percentage of true negatives 100%; accuracy (true positives plus true negatives over the totality of patients) 93,3%; and Cohen's kappa index 0,84. CONCLUSION: Context-dependent associative memories can operate as medical expert systems. The model is presented in a simple and tutorial way to encourage straightforward implementations by medical groups. An application with real data, presented as a primary evaluation of the validity and potentiality of the model in medical diagnosis, shows that the model is a highly promising alternative in the development of accuracy diagnostic tools. [Abstract/Link to Full Text]

Perel P, Edwards P, Wentz R, Roberts I
Systematic review of prognostic models in traumatic brain injury.
BMC Med Inform Decis Mak. 2006;638.
BACKGROUND: Traumatic brain injury (TBI) is a leading cause of death and disability world-wide. The ability to accurately predict patient outcome after TBI has an important role in clinical practice and research. Prognostic models are statistical models that combine two or more items of patient data to predict clinical outcome. They may improve predictions in TBI patients. Multiple prognostic models for TBI have accumulated for decades but none of them is widely used in clinical practice. The objective of this systematic review is to critically assess existing prognostic models for TBI METHODS: Studies that combine at least two variables to predict any outcome in patients with TBI were searched in PUBMED and EMBASE. Two reviewers independently examined titles, abstracts and assessed whether each met the pre-defined inclusion criteria. RESULTS: A total of 53 reports including 102 models were identified. Almost half (47%) were derived from adult patients. Three quarters of the models included less than 500 patients. Most of the models (93%) were from high income countries populations. Logistic regression was the most common analytical strategy to derived models (47%). In relation to the quality of the derivation models (n:66), only 15% reported less than 10% pf loss to follow-up, 68% did not justify the rationale to include the predictors, 11% conducted an external validation and only 19% of the logistic models presented the results in a clinically user-friendly way CONCLUSION: Prognostic models are frequently published but they are developed from small samples of patients, their methodological quality is poor and they are rarely validated on external populations. Furthermore, they are not clinically practical as they are not presented to physicians in a user-friendly way. Finally because only a few are developed using populations from low and middle income countries, where most of trauma occurs, the generalizability to these setting is limited. [Abstract/Link to Full Text]

Ramnarayan P, Winrow A, Coren M, Nanduri V, Buchdahl R, Jacobs B, Fisher H, Taylor PM, Wyatt JC, Britto J
Diagnostic omission errors in acute paediatric practice: impact of a reminder system on decision-making.
BMC Med Inform Decis Mak. 2006;637.
BACKGROUND: Diagnostic error is a significant problem in specialities characterised by diagnostic uncertainty such as primary care, emergency medicine and paediatrics. Despite wide-spread availability, computerised aids have not been shown to significantly improve diagnostic decision-making in a real world environment, mainly due to the need for prolonged system consultation. In this study performed in the clinical environment, we used a Web-based diagnostic reminder system that provided rapid advice with free text data entry to examine its impact on clinicians' decisions in an acute paediatric setting during assessments characterised by diagnostic uncertainty. METHODS: Junior doctors working over a 5-month period at four paediatric ambulatory units consulted the Web-based diagnostic aid when they felt the need for diagnostic assistance. Subjects recorded their clinical decisions for patients (differential diagnosis, test-ordering and treatment) before and after system consultation. An expert panel of four paediatric consultants independently suggested clinically significant decisions indicating an appropriate and 'safe' assessment. The primary outcome measure was change in the proportion of 'unsafe' workups by subjects during patient assessment. A more sensitive evaluation of impact was performed using specific validated quality scores. Adverse effects of consultation on decision-making, as well as the additional time spent on system use were examined. RESULTS: Subjects attempted to access the diagnostic aid on 595 occasions during the study period (8.6% of all medical assessments); subjects examined diagnostic advice only in 177 episodes (30%). Senior House Officers at hospitals with greater number of available computer workstations in the clinical area were most likely to consult the system, especially out of working hours. Diagnostic workups construed as 'unsafe' occurred in 47/104 cases (45.2%); this reduced to 32.7% following system consultation (McNemar test, p < 0.001). Subjects' mean 'unsafe' workups per case decreased from 0.49 to 0.32 (p < 0.001). System advice prompted the clinician to consider the 'correct' diagnosis (established at discharge) during initial assessment in 3/104 patients. Median usage time was 1 min 38 sec (IQR 50 sec-3 min 21 sec). Despite a modest increase in the number of diagnostic possibilities entertained by the clinician, no adverse effects were demonstrable on patient management following system use. Numerous technical barriers prevented subjects from accessing the diagnostic aid in the majority of eligible patients in whom they sought diagnostic assistance. CONCLUSION: We have shown that junior doctors used a Web-based diagnostic reminder system during acute paediatric assessments to significantly improve the quality of their diagnostic workup and reduce diagnostic omission errors. These benefits were achieved without any adverse effects on patient management following a quick consultation. [Abstract/Link to Full Text]

Muin M, Fontelo P
Technical development of PubMed interact: an improved interface for MEDLINE/PubMed searches.
BMC Med Inform Decis Mak. 2006;636.
BACKGROUND: The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. RESULTS: PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. CONCLUSION: PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications. [Abstract/Link to Full Text]

Nystr�m M, Merkel M, Ahrenberg L, Zweigenbaum P, Petersson H, Ahlfeldt H
Creating a medical English-Swedish dictionary using interactive word alignment.
BMC Med Inform Decis Mak. 2006;635.
BACKGROUND: This paper reports on a parallel collection of rubrics from the medical terminology systems ICD-10, ICF, MeSH, NCSP and KSH97-P and its use for semi-automatic creation of an English-Swedish dictionary of medical terminology. The methods presented are relevant for many other West European language pairs than English-Swedish. METHODS: The medical terminology systems were collected in electronic format in both English and Swedish and the rubrics were extracted in parallel language pairs. Initially, interactive word alignment was used to create training data from a sample. Then the training data were utilised in automatic word alignment in order to generate candidate term pairs. The last step was manual verification of the term pair candidates. RESULTS: A dictionary of 31,000 verified entries has been created in less than three man weeks, thus with considerably less time and effort needed compared to a manual approach, and without compromising quality. As a side effect of our work we found 40 different translation problems in the terminology systems and these results indicate the power of the method for finding inconsistencies in terminology translations. We also report on some factors that may contribute to making the process of dictionary creation with similar tools even more expedient. Finally, the contribution is discussed in relation to other ongoing efforts in constructing medical lexicons for non-English languages. CONCLUSION: In three man weeks we were able to produce a medical English-Swedish dictionary consisting of 31,000 entries and also found hidden translation errors in the utilized medical terminology systems. [Abstract/Link to Full Text]

Shah A, Jacobs DO, Martins H, Harker M, Menezes A, McCready M, Pietrobon R
DADOS-Survey: an open-source application for CHERRIES-compliant Web surveys.
BMC Med Inform Decis Mak. 2006;634.
BACKGROUND: The Internet has been increasingly utilized in biomedical research. From online searching for literature to data sharing, the Internet has emerged as a primary means of research for many physicians and scientists. As a result, Web-based surveys have been employed as an alternative to traditional, paper-based surveys. We describe DADOS-Survey, an open-source Web-survey application developed at our institution that, to the best of our knowledge, is the first to be compliant with the Checklist for Reporting Results of Internet E-Surveys (CHERRIES). DADOS-Survey was designed with usability as a priority, allowing investigators to design and execute their own studies with minimal technical difficulties in doing so. RESULTS: To date, DADOS-Survey has been successfully implemented in five Institutional Review Board-approved studies conducted by various departments within our academic center. Each of these studies employed a Web-survey design as their primary methodology. Our initial experience indicates that DADOS-Survey has been used with relative ease by each of the investigators and survey recipients. This has been further demonstrated through formal and field usability testing, during which time suggestions for improvement were incorporated into the software design. CONCLUSION: DADOS-Survey has the potential to have an important role in the future direction of Web-survey administration in biomedical research. This CHERRIES-compliant application is tailored to the emerging requirements of quality data collection in medicine. [Abstract/Link to Full Text]

Coiera E, Magrabi F, Westbrook JI, Kidd MR, Day RO
Protocol for the Quick Clinical study: a randomised controlled trial to assess the impact of an online evidence retrieval system on decision-making in general practice.
BMC Med Inform Decis Mak. 2006;633.
BACKGROUND: Online information retrieval systems have the potential to improve patient care but there are few comparative studies of the impact of online evidence on clinicians' decision-making behaviour in routine clinical work. METHODS/DESIGN: A randomized controlled parallel design is employed to assess the effectiveness of an online evidence retrieval system, Quick Clinical (QC) in improving clinical decision-making processes in general practice. Eligible clinicians are randomised either to receive access or not to receive access to QC in their consulting rooms for 12 months. Participants complete pre- and post trial surveys.Two-hundred general practitioners are recruited. Participants must be registered to practice in Australia, have a computer with Internet access in their consulting room and use electronic prescribing. Clinicians planning to retire or move to another practice within 12 months or participating in any other clinical trial involving electronic extraction of prescriptions data are excluded from the study.The primary end-points for the study is clinician acceptance and use of QC and the resulting change in decision-making behaviour. The study will examine prescribing patterns related to frequently prescribed medications where there has been a recent significant shift in recommendations regarding their use based upon new evidence. Secondary outcome measures include self-reported changes in diagnosis, patient education, prescriptions written, investigations and referrals. DISCUSSION: A trial under experimental conditions is an effective way of examining the impact of using QC in routine general practice consultations. [Abstract/Link to Full Text]

Pietrobon R, Shah A, Kuo P, Harker M, McCready M, Butler C, Martins H, Moorman CT, Jacobs DO
Duke Surgery Research Central: an open-source Web application for the improvement of compliance with research regulation.
BMC Med Inform Decis Mak. 2006;632.
BACKGROUND: Although regulatory compliance in academic research is enforced by law to ensure high quality and safety to participants, its implementation is frequently hindered by cost and logistical barriers. In order to decrease these barriers, we have developed a Web-based application, Duke Surgery Research Central (DSRC), to monitor and streamline the regulatory research process. RESULTS: The main objective of DSRC is to streamline regulatory research processes. The application was built using a combination of paper prototyping for system requirements and Java as the primary language for the application, in conjunction with the Model-View-Controller design model. The researcher interface was designed for simplicity so that it could be used by individuals with different computer literacy levels. Analogously, the administrator interface was designed with functionality as its primary goal. DSRC facilitates the exchange of regulatory documents between researchers and research administrators, allowing for tasks to be tracked and documents to be stored in a Web environment accessible from an Intranet. Usability was evaluated using formal usability tests and field observations. Formal usability results demonstrated that DSRC presented good speed, was easy to learn and use, had a functionality that was easily understandable, and a navigation that was intuitive. Additional features implemented upon request by initial users included: extensive variable categorization (in contrast with data capture using free text), searching capabilities to improve how research administrators could search an extensive number of researcher names, warning messages before critical tasks were performed (such as deleting a task), and confirmatory e-mails for critical tasks (such as completing a regulatory task). CONCLUSION: The current version of DSRC was shown to have excellent overall usability properties in handling research regulatory issues. It is hoped that its release as an open-source application will promote improved and streamlined regulatory processes for individual academic centers as well as larger research networks. [Abstract/Link to Full Text]

Westbrook JI, Westbrook MT, Gosling AS
Ambulance officers' use of online clinical evidence.
BMC Med Inform Decis Mak. 2006;631.
BACKGROUND: Hospital-based clinicians have been shown to use and attain benefits from online evidence systems. To our knowledge there have been no studies investigating whether and how ambulance officers use online evidence systems if provided. We surveyed ambulance officers to examine their knowledge and use of the Clinical Information Access Program (CIAP), an online evidence system providing 24-hour access to information to support evidence-based practice. METHODS: A questionnaire was completed by 278 ambulance officers in New South Wales, Australia. Comparisons were made between those who used CIAP and officers who had heard of, but not used CIAP. RESULTS: Half the sample (48.6%) knew of, and 28.8% had used CIAP. Users were more likely to have heard of CIAP from a CIAP representative/presentation, non-users from written information. Compared to ambulance officers who had heard of but had not used CIAP, users were more likely to report better computer skills and that their supervisors regarded use of CIAP as a legitimate part of ambulance officers' clinical role. The main reasons for non-use were lack of access(49.0%) and training(31.4%). Of users, 51.3% rated their skills at finding information as good/very good, 67.5% found the information sought all/most of the time, 87.3% believed CIAP had the potential to improve patient care and 28.2% had directly experienced this. Most access to CIAP occurred at home. The databases frequently accessed were MIMS (A medicines information database) (73.8%) and MEDLINE(67.5%). The major journals accessed were Journal of Emergency Nursing(37.5%), American Journal of Medicine(30.0%) and JAMA(27.5%). CONCLUSION: Over half of ambulance officers had not heard of CIAP. The proportion who knew about and used CIAP was also low. Reasons for this appear to be a work culture not convinced of CIAP's relevance to pre-hospital patient care and lack of access to CIAP at work. Ambulance officers who used CIAP accessed it primarily from home and valued it highly. Lack of access to CIAP at central work locations deprives ambulance officers of many of the benefits of an online evidence system. [Abstract/Link to Full Text]

Zeng QT, Goryachev S, Weiss S, Sordo M, Murphy SN, Lazarus R
Extracting principal diagnosis, co-morbidity and smoking status for asthma research: evaluation of a natural language processing system.
BMC Med Inform Decis Mak. 2006;630.
BACKGROUND: The text descriptions in electronic medical records are a rich source of information. We have developed a Health Information Text Extraction (HITEx) tool and used it to extract key findings for a research study on airways disease. METHODS: The principal diagnosis, co-morbidity and smoking status extracted by HITEx from a set of 150 discharge summaries were compared to an expert-generated gold standard. RESULTS: The accuracy of HITEx was 82% for principal diagnosis, 87% for co-morbidity, and 90% for smoking status extraction, when cases labeled "Insufficient Data" by the gold standard were excluded. CONCLUSION: We consider the results promising, given the complexity of the discharge summaries and the extraction tasks. [Abstract/Link to Full Text]

Bleeker SE, Derksen-Lubsen G, van Ginneken AM, van der Lei J, Moll HA
Structured data entry for narrative data in a broad specialty: patient history and physical examination in pediatrics.
BMC Med Inform Decis Mak. 2006;629.
BACKGROUND: Whereas an electronic medical record (EMR) system can partly address the limitations, of paper-based documentation, such as fragmentation of patient data, physical paper records missing and poor legibility, structured data entry (SDE, i.e. data entry based on selection of predefined medical concepts) is essential for uniformity of data, easier reporting, decision support, quality assessment, and patient-oriented clinical research. The aim of this project was to explore whether a previously developed generic (i.e. content independent) SDE application to support the structured documentation of narrative data (called OpenSDE) can be used to model data obtained at history taking and physical examination of a broad specialty. METHODS: OpenSDE was customized for the broad domain of general pediatrics: medical concepts and its descriptors from history taking and physical examination were modeled into a tree structure. RESULTS: An EMR system allowing structured recording (OpenSDE) of pediatric narrative data was developed. Patient history is described by 20 main concepts and physical examination by 11. In total, the thesaurus consists of about 1800 items, used in 8648 nodes in the tree with a maximum depth of 9 levels. Patient history contained 6312 nodes, and physical examination 2336. User-defined entry forms can be composed according to individual needs, without affecting the underlying data representation. The content of the tree can be adjusted easily and sharing records among different disciplines is possible. Data that are relevant in more than one context can be accessed from multiple branches of the tree without duplication or ambiguity of data entry via "shortcuts". CONCLUSION: An expandable EMR system with structured data entry (OpenSDE) for pediatrics was developed, allowing structured documentation of patient history and physical examination. For further evaluation in other environments, the tree structure for general pediatrics is available at the Erasmus MC Web site (in Dutch, translation into English in progress) 1. The generic OpenSDE application is available at the OpenSDE Web site 2. [Abstract/Link to Full Text]

Bj�rk J, Forberg JL, Ohlsson M, Edenbrandt L, Ohlin H, Ekelund U
A simple statistical model for prediction of acute coronary syndrome in chest pain patients in the emergency department.
BMC Med Inform Decis Mak. 2006;628.
BACKGROUND: Several models for prediction of acute coronary syndrome (ACS) among chest pain patients in the emergency department (ED) have been presented, but many models predict only the likelihood of acute myocardial infarction, or include a large number of variables, which make them less than optimal for implementation at a busy ED. We report here a simple statistical model for ACS prediction that could be used in routine care at a busy ED. METHODS: Multivariable analysis and logistic regression were used on data from 634 ED visits for chest pain. Only data immediately available at patient presentation were used. To make ACS prediction stable and the model useful for personnel inexperienced in electrocardiogram (ECG) reading, simple ECG data suitable for computerized reading were included. RESULTS: Besides ECG, eight variables were found to be important for ACS prediction, and included in the model: age, chest discomfort at presentation, symptom duration and previous hypertension, angina pectoris, AMI, congestive heart failure or PCI/CABG. At an ACS prevalence of 21% and a set sensitivity of 95%, the negative predictive value of the model was 96%. CONCLUSION: The present prediction model, combined with the clinical judgment of ED personnel, could be useful for the early discharge of chest pain patients in populations with a low prevalence of ACS. [Abstract/Link to Full Text]

Jafari P, Azuaje F
An assessment of recently published gene expression data analyses: reporting experimental design and statistical factors.
BMC Med Inform Decis Mak. 2006;627.
BACKGROUND: The analysis of large-scale gene expression data is a fundamental approach to functional genomics and the identification of potential drug targets. Results derived from such studies cannot be trusted unless they are adequately designed and reported. The purpose of this study is to assess current practices on the reporting of experimental design and statistical analyses in gene expression-based studies. METHODS: We reviewed hundreds of MEDLINE-indexed papers involving gene expression data analysis, which were published between 2003 and 2005. These papers were examined on the basis of their reporting of several factors, such as sample size, statistical power and software availability. RESULTS: Among the examined papers, we concentrated on 293 papers consisting of applications and new methodologies. These papers did not report approaches to sample size and statistical power estimation. Explicit statements on data transformation and descriptions of the normalisation techniques applied prior to data analyses (e.g. classification) were not reported in 57 (37.5%) and 104 (68.4%) of the methodology papers respectively. With regard to papers presenting biomedical-relevant applications, 41(29.1 %) of these papers did not report on data normalisation and 83 (58.9%) did not describe the normalisation technique applied. Clustering-based analysis, the t-test and ANOVA represent the most widely applied techniques in microarray data analysis. But remarkably, only 5 (3.5%) of the application papers included statements or references to assumption about variance homogeneity for the application of the t-test and ANOVA. There is still a need to promote the reporting of software packages applied or their availability. CONCLUSION: Recently-published gene expression data analysis studies may lack key information required for properly assessing their design quality and potential impact. There is a need for more rigorous reporting of important experimental factors such as statistical power and sample size, as well as the correct description and justification of statistical methods applied. This paper highlights the importance of defining a minimum set of information required for reporting on statistical design and analysis of expression data. By improving practices of statistical analysis reporting, the scientific community can facilitate quality assurance and peer-review processes, as well as the reproducibility of results. [Abstract/Link to Full Text]

Wu RC, Straus SE
Evidence for handheld electronic medical records in improving care: a systematic review.
BMC Med Inform Decis Mak. 2006;626.
BACKGROUND: Handheld electronic medical records are expected to improve physician performance and patient care. To confirm this, we performed a systematic review of the evidence assessing the effects of handheld electronic medical records on clinical care. METHODS: To conduct the systematic review, we searched MEDLINE, EMBASE, CINAHL, and the Cochrane library from 1966 through September 2005. We included randomized controlled trials that evaluated effects on practitioner performance or patient outcomes of handheld electronic medical records compared to either paper medical records or desktop electronic medical records. Two reviewers independently reviewed citations, assessed full text articles and abstracted data from the studies. RESULTS: Two studies met our inclusion criteria. No other randomized controlled studies or non-randomized controlled trials were found that met our inclusion criteria. Both studies were methodologically strong. The studies examined changes in documentation in orthopedic patients with handheld electronic medical records compared to paper charts, and both found an increase in documentation. Other effects noted with handheld electronic medical records were an increase in time to document and an increase in wrong or redundant diagnoses. CONCLUSION: Handheld electronic medical records may improve documentation, but as yet, the number of studies is small and the data is restricted to one group of patients and a small group of practitioners. Further study is required to determine the benefits with handheld electronic medical records especially in assessing clinical outcomes. [Abstract/Link to Full Text]

Tobias J, Chilukuri R, Komatsoulis GA, Mohanty S, Sioutos N, Warzel DB, Wright LW, Crowley RS
The CAP cancer protocols--a case study of caCORE based data standards implementation to integrate with the Cancer Biomedical Informatics Grid.
BMC Med Inform Decis Mak. 2006;625.
BACKGROUND: The Cancer Biomedical Informatics Grid (caBIG) is a network of individuals and institutions, creating a world wide web of cancer research. An important aspect of this informatics effort is the development of consistent practices for data standards development, using a multi-tier approach that facilitates semantic interoperability of systems. The semantic tiers include (1) information models, (2) common data elements, and (3) controlled terminologies and ontologies. The College of American Pathologists (CAP) cancer protocols and checklists are an important reporting standard in pathology, for which no complete electronic data standard is currently available. METHODS: In this manuscript, we provide a case study of Cancer Common Ontologic Representation Environment (caCORE) data standard implementation of the CAP cancer protocols and checklists model--an existing and complex paper based standard. We illustrate the basic principles, goals and methodology for developing caBIG models. RESULTS: Using this example, we describe the process required to develop the model, the technologies and data standards on which the process and models are based, and the results of the modeling effort. We address difficulties we encountered and modifications to caCORE that will address these problems. In addition, we describe four ongoing development projects that will use the emerging CAP data standards to achieve integration of tissue banking and laboratory information systems. CONCLUSION: The CAP cancer checklists can be used as the basis for an electronic data standard in pathology using the caBIG semantic modeling methodology. [Abstract/Link to Full Text]

Jones TH, Hanney S, Buxton MJ
The journals of importance to UK clinicians: a questionnaire survey of surgeons.
BMC Med Inform Decis Mak. 2006;624.
BACKGROUND: Peer-reviewed journals are seen as a major vehicle in the transmission of research findings to clinicians. Perspectives on the importance of individual journals vary and the use of impact factors to assess research is criticised. Other surveys of clinicians suggest a few key journals within a specialty, and sub-specialties, are widely read. Journals with high impact factors are not always widely read or perceived as important. In order to determine whether UK surgeons consider peer-reviewed journals to be important information sources and which journals they read and consider important to inform their clinical practice, we conducted a postal questionnaire survey and then compared the findings with those from a survey of US surgeons. METHODS: A questionnaire survey sent to 2,660 UK surgeons asked which information sources they considered to be important and which peer-reviewed journals they read, and perceived as important, to inform their clinical practice. Comparisons were made with numbers of UK NHS-funded surgery publications, journal impact factors and other similar surveys. RESULTS: Peer-reviewed journals were considered to be the second most important information source for UK surgeons. A mode of four journals read was found with academics reading more than non-academics. Two journals, the BMJ and the Annals of the Royal College of Surgeons of England, are prominent across all sub-specialties and others within sub-specialties. The British Journal of Surgery plays a key role within three sub-specialties. UK journals are generally preferred and readership patterns are influenced by membership journals. Some of the journals viewed by surgeons as being most important, for example the Annals of the Royal College of Surgeons of England, do not have high impact factors. CONCLUSION: Combining the findings from this study with comparable studies highlights the importance of national journals and of membership journals. Our study also illustrates the complexity of the link between the impact factors of journals and the importance of the journals to clinicians. This analysis potentially provides an additional basis on which to assess the role of different journals, and the published output from research. [Abstract/Link to Full Text]

Lane SJ, Heddle NM, Arnold E, Walker I
A review of randomized controlled trials comparing the effectiveness of hand held computers with paper methods for data collection.
BMC Med Inform Decis Mak. 2006;623.
BACKGROUND: Handheld computers are increasingly favoured over paper and pencil methods to capture data in clinical research. METHODS: This study systematically identified and reviewed randomized controlled trials (RCTs) that compared the two methods for self-recording and reporting data, and where at least one of the following outcomes was assessed: data accuracy; timeliness of data capture; and adherence to protocols for data collection. RESULTS: A comprehensive key word search of NLM Gateway's database yielded 9 studies fitting the criteria for inclusion. Data extraction was performed and checked by two of the authors. None of the studies included all outcomes. The results overall, favor handheld computers over paper and pencil for data collection among study participants but the data are not uniform for the different outcomes. Handheld computers appear superior in timeliness of receipt and data handling (four of four studies) and are preferred by most subjects (three of four studies). On the other hand, only one of the trials adequately compared adherence to instructions for recording and submission of data (handheld computers were superior), and comparisons of accuracy were inconsistent between five studies. CONCLUSION: Handhelds are an effective alternative to paper and pencil modes of data collection; they are faster and were preferred by most users. [Abstract/Link to Full Text]

Ramnarayan P, Roberts GC, Coren M, Nanduri V, Tomlinson A, Taylor PM, Wyatt JC, Britto JF
Assessment of the potential impact of a reminder system on the reduction of diagnostic errors: a quasi-experimental study.
BMC Med Inform Decis Mak. 2006;622.
BACKGROUND: Computerized decision support systems (DSS) have mainly focused on improving clinicians' diagnostic accuracy in unusual and challenging cases. However, since diagnostic omission errors may predominantly result from incomplete workup in routine clinical practice, the provision of appropriate patient- and context-specific reminders may result in greater impact on patient safety. In this experimental study, a mix of easy and difficult simulated cases were used to assess the impact of a novel diagnostic reminder system (ISABEL) on the quality of clinical decisions made by various grades of clinicians during acute assessment. METHODS: Subjects of different grades (consultants, registrars, senior house officers and medical students), assessed a balanced set of 24 simulated cases on a trial website. Subjects recorded their clinical decisions for the cases (differential diagnosis, test-ordering and treatment), before and after system consultation. A panel of two pediatric consultants independently provided gold standard responses for each case, against which subjects' quality of decisions was measured. The primary outcome measure was change in the count of diagnostic errors of omission (DEO). A more sensitive assessment of the system's impact was achieved using specific quality scores; additional consultation time resulting from DSS use was also calculated. RESULTS: 76 subjects (18 consultants, 24 registrars, 19 senior house officers and 15 students) completed a total of 751 case episodes. The mean count of DEO fell from 5.5 to 5.0 across all subjects (repeated measures ANOVA, p < 0.001); no significant interaction was seen with subject grade. Mean diagnostic quality score increased after system consultation (0.044; 95% confidence interval 0.032, 0.054). ISABEL reminded subjects to consider at least one clinically important diagnosis in 1 in 8 case episodes, and prompted them to order an important test in 1 in 10 case episodes. Median extra time taken for DSS consultation was 1 min (IQR: 30 sec to 2 min). CONCLUSION: The provision of patient- and context-specific reminders has the potential to reduce diagnostic omissions across all subject grades for a range of cases. This study suggests a promising role for the use of future reminder-based DSS in the reduction of diagnostic error. [Abstract/Link to Full Text]

Diero L, Rotich JK, Bii J, Mamlin BW, Einterz RM, Kalamai IZ, Tierney WM
A computer-based medical record system and personal digital assistants to assess and follow patients with respiratory tract infections visiting a rural Kenyan health centre.
BMC Med Inform Decis Mak. 2006;621.
BACKGROUND: Clinical research can be facilitated by the use of informatics tools. We used an existing electronic medical record (EMR) system and personal data assistants (PDAs) to assess the characteristics and outcomes of patients with acute respiratory illnesses (ARIs) visiting a Kenyan rural health center. METHODS: We modified the existing EMR to include details on patients with ARIs. The EMR database was then used to identify patients with ARIs who were prospectively followed up by a research assistant who rode a bicycle to patients' homes and entered data into a PDA. RESULTS: A total of 2986 clinic visits for 2009 adult patients with respiratory infections were registered in the database between August 2002 and January 2005; 433 patients were selected for outcome assessments. These patients were followed up in the villages and assessed at 7 and 30 days later. Complete follow-up data were obtained on 381 patients (88%) and merged with data from the enrollment visit's electronic medical records and subsequent health center visits to assess duration of illness and complications. Symptoms improved at 7 and 30 days, but a substantial minority of patients had persistent symptoms. Eleven percent of patients sought additional care for their respiratory infection. CONCLUSION: EMRs and PDA are useful tools for performing prospective clinical research in resource constrained developing countries. [Abstract/Link to Full Text]

Recent Articles in Bulletin of the Medical Library Association

Hollander S, Lanier D
The physician-patient relationship in an electronic environment: a regional snapshot.
Bull Med Libr Assoc. 2001 Oct;89(4):397-9. [Abstract/Link to Full Text]

Olmstadt W, Foster CL, Burford NG, Funkhouser NF, Jaros J
Clinical veterinary librarianship--the Texas A&M University experience.
Bull Med Libr Assoc. 2001 Oct;89(4):395-7. [Abstract/Link to Full Text]

Belleh GS, Luft E
Financing North American medical libraries in the nineteenth century.
Bull Med Libr Assoc. 2001 Oct;89(4):386-94.
Culture not only justifies the existence of libraries but also determines the level of funding libraries receive for development. Cultural appreciation of the importance of libraries encourages their funding; lack of such appreciation discourages it. Medical library development is driven by culture in general and the culture of physicians in particular. Nineteenth-century North American medical library funding reflected the impact of physician culture in three phases: (1) Before the dawn of anesthesia (1840s) and antisepsis (1860s), when the wisdom of elders contained in books was venerated, libraries were well supported. (2) In the last third of the nineteenth century, as modern medicine grew and as physicians emphasized the practical and the present, rather than books, support for medical libraries declined. (3) By the 1890s, this attitude had changed because physicians had come to realize that, without both old and new medical literature readily available, they could not keep up with rapidly changing current clinical practice or research. Thus, "The Medical Library Movement" heralded the turn of the century. [Abstract/Link to Full Text]

Brown CD, MacCall S
Coping with a MEDLIB-L service outage.
Bull Med Libr Assoc. 2001 Oct;89(4):379-85.
OBJECTIVE: The study assessed the coping strategies of MEDLIB-L subscribers during an unexpected disruption in the list's service. METHODS: An online survey of MEDLIB-L subscribers was performed following a six-day service outage in August 1999. RESULTS: Respondents' information needs resulted in two distinct coping strategies. Subscribers without a recognized information need or an information need determined to be not pressing coped by waiting out the interruption. Subscribers with pressing information needs turned to alternative methods of resolving these needs. CONCLUSIONS: While most respondents missed the list and the assistance that it provided, many did not feel that the outage required significant coping strategies. The outage was viewed as a "minor stressor" and did not require secondary-level assessment of the availability and suitability of alternative resources. [Abstract/Link to Full Text]

De Groote SL, Dorsch JL
Online journals: impact on print journal usage.
Bull Med Libr Assoc. 2001 Oct;89(4):372-8.
PURPOSE: The research sought to determine the impact of online journals on the use of print journals and interlibrary loan (ILL). SETTING: The Library of the Health Sciences-Peoria is a regional site of the University of Illinois at Chicago (UIC) Library with a print journal collection of approximately 400 titles. Since 1999, UIC site licenses have given students and faculty affiliated with UIC-Peoria access to more than 4,000 online full-text journal titles through the Internet. METHODOLOGY: The Library of the Health Sciences-Peoria has conducted a journal-use study over an extended period of time. The information collected from this study was used to assess the impact of 104 online journals, added to the collection in January 1999, on the use of print journals. RESULTS: Results of the statistical analysis showed print journal usage decreased significantly since the introduction of online journals (F(1,147) = 12.10, P < 0.001). This decrease occurred regardless of whether a journal was available only in print or both online and in print. Interlibrary loan requests have also significantly decreased since the introduction of online journals (F(2,30) = 4.46, P < 0.02). CONCLUSIONS: The decrease in use of the print collection suggests that many patrons prefer to access journals online. The negative impact the online journals have had on the use of the journal titles available only in print suggests users may be compromising quality for convenience when selecting journal articles. Possible implications for collection development are discussed. [Abstract/Link to Full Text]

Chen FL, Wrynn P, Rieke JL
Electronic journal access: how does it affect the print subscription price?
Bull Med Libr Assoc. 2001 Oct;89(4):363-71.
OBJECTIVE: This study examined the rates of print journal subscription price increases according to the type of available electronic access. The types of access included: electronic priced separately from the print, combination print with "free online" access, and aggregated, defined here as electronic access purchased as part of a collection. The percentages of print price increases were compared to each other and to that for titles available only in print. The authors were not aware of prior objective research in this area. METHODS: The authors analyzed the percentage print price increases of 300 journals over a five-year time period. The titles were grouped according to type of available electronic access. The median and mean percentage print price increases were calculated and plotted for all titles within each group. RESULTS: Using both the median and the mean to look at the percentage print price increases over five years, it was obvious that print prices for journals with electronic access exceeded journals that did not offer an electronic option. Electronic priced separately averaged 3% to 5% higher than print only titles using both measures. Combination print with "free online" access had higher increases from 1996 to 1999, but, in 2000, their percentage increases were about the same as print only titles. The rate of price increases for aggregated titles consistently went down over the past five years. Journals with no electronic option showed the lowest percentage rates of print price increase. CONCLUSIONS: The authors' findings reveal that the increases of print prices for their sample of titles were higher if a type of electronic access was offered. According to the results of this study, aggregated collections currently represent the electronic option whose percentage price increase for print prices was lowest. However, the uneven fluctuations in rates of subscription prices revealed that the pricing of journals with electronic access is still evolving. More study is recommended to see if the trends observed in this study are sustained over a longer time period. [Abstract/Link to Full Text]

Brettle AJ, Long AF
Comparison of bibliographic databases for information on the rehabilitation of people with severe mental illness.
Bull Med Libr Assoc. 2001 Oct;89(4):353-62.
OBJECTIVE: The research sought to examine the overlap in coverage between several health-related databases, thus enabling the identification of the most important sources for searching for information on the rehabilitation of people with severe mental illness. METHODS: The literature was searched within a systematic review. Several health-related databases were retrieved (Cumulative Index to Nursing and Allied Health Literature, The Cochrane Library, MEDLINE, PsycLIT, Sociofile, and Social Science Citation Index), noting their source and comparing results retrieved from each database. FINDINGS: The total number of studies retrieved from each database varied. Almost a third of the papers retrieved from each database were unique to that source. Forty-two percent of the papers were only found in one database. Restricting a search to one database alone would miss many papers and could affect the results of a systematic review. PsycLIT was the most useful database for this topic area, containing 44% of the papers. MEDLINE, the database of first choice for many health professionals, held only 29%. CONCLUSIONS: No database was determined to be significantly more useful than any other--each warranted inclusion in the study. Reliance cannot be placed on one database alone, and other methods such as hand searching should also be used. Although this may not be new information for information professionals, it is likely to be new for health professionals and researchers who are increasingly performing their own literature searches. Information professionals have an important role to play in conveying this message to those outside their profession. [Abstract/Link to Full Text]

Helmer D, Savoie I, Green C, Kazanjian A
Evidence-based practice: extending the search to find material for the systematic review.
Bull Med Libr Assoc. 2001 Oct;89(4):346-52.
BACKGROUND: Cochrane-style systematic reviews increasingly require the participation of librarians. Guidelines on the appropriate search strategy to use for systematic reviews have been proposed. However, research evidence supporting these recommendations is limited. OBJECTIVE: This study investigates the effectiveness of various systematic search methods used to uncover randomized controlled trials (RCTs) for systematic reviews. Effectiveness is defined as the proportion of relevant material uncovered for the systematic review using extended systematic review search methods. The following extended systematic search methods are evaluated: searching subject-specific or specialized databases (including trial registries), hand searching, scanning reference lists, and communicating personally. METHODS: Two systematic review projects were prospectively monitored regarding the method used to identify items as well as the type of items retrieved. The proportion of RCTs identified by each systematic search method was calculated. RESULTS: The extended systematic search methods uncovered 29.2% of all items retrieved for the systematic reviews. The search of specialized databases was the most effective method, followed by scanning of reference lists, communicating personally, and hand searching. Although the number of items identified through hand searching was small, these unique items would otherwise have been missed. CONCLUSIONS: Extended systematic search methods are effective tools for uncovering material for the systematic review. The quality of the items uncovered has yet to be assessed and will be key in evaluating the value of the systematic search methods. [Abstract/Link to Full Text]

Fuller DM, Hinegardner PG
Ensuring quality Website redesign: the University of Maryland's experience.
Bull Med Libr Assoc. 2001 Oct;89(4):339-45.
The Web Redesign Committee at the Health Sciences and Human Services Library (HS/HSL) of the University of Maryland was formed to evaluate its site and oversee the site's redesign. The committee's goal was to design a site that would be functional, be usable, and provide the library with a more current image. Based on a literature review and discussions with colleagues, a usability study was conducted to gain a better understanding of how the Website was used. Volunteers from across the campus participated in the study. A Web-based survey was also used to gather feedback. To complement user input, library staff were asked to review the existing site. A prototype site was developed incorporating suggestions obtained from the evaluation mechanisms. The usability study was particularly useful because it identified problem areas, including terminology, which would have been overlooked by library staff. A second usability study was conducted to refine the prototype. The new site was launched in the spring of 2000. The usability studies were valuable mechanisms in designing the site. Users felt invested in the project, and the committee received valuable feedback. This process led to an improved Website and higher visibility for the library on campus. [Abstract/Link to Full Text]

Duncan JM, Roth LK
Production of the next-generation library virtual tour.
Bull Med Libr Assoc. 2001 Oct;89(4):331-8.
While many libraries offer overviews of their services through their Websites, only a small number of health sciences libraries provide Web-based virtual tours. These tours typically feature photographs of major service areas along with textual descriptions. This article describes the process for planning, producing, and implementing a next-generation virtual tour in which a variety of media elements are integrated: photographic images, 360-degree "virtual reality" views, textual descriptions, and contextual floor plans. Hardware and software tools used in the project are detailed, along with a production timeline and budget, tips for streamlining the process, and techniques for improving production. This paper is intended as a starting guide for other libraries considering an investment in such a project. [Abstract/Link to Full Text]

Marshall JG
Carol G. Jenkins, Medical Library Association President 2001-2002.
Bull Med Libr Assoc. 2001 Jul;89(3):311-4. [Abstract/Link to Full Text]

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

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

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

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

Lipscomb CE
Mergers in the publishing industry.
Bull Med Libr Assoc. 2001 Jul;89(3):307-8. [Abstract/Link to Full Text]

Plutchak TS
Publishers.
Bull Med Libr Assoc. 2001 Jul;89(3):303-5. [Abstract/Link to Full Text]

Darmoni SJ, Thirion B, Leroy JP, Douy�re M
The use of Dublin Core metadata in a structured health resource guide on the internet.
Bull Med Libr Assoc. 2001 Jul;89(3):297-301. [Abstract/Link to Full Text]

Ash JS, Gorman PN, Lavelle M, Lyman J, Delcambre LM, Maier D, Bowers S, Weaver M
Bundles: meeting clinical information needs.
Bull Med Libr Assoc. 2001 Jul;89(3):294-6. [Abstract/Link to Full Text]

Al-Ansari HA, Al-Enezi S
Health sciences libraries in Kuwait: a study of their resources, facilities, and services.
Bull Med Libr Assoc. 2001 Jul;89(3):287-93.
The purpose of this study was to examine the current status of health sciences libraries in Kuwait in terms of their staff, collections, facilities, use of information technology, information services, and cooperation. Seventeen libraries participated in the study. Results show that the majority of health sciences libraries were established during the 1980s. Their collections are relatively small. The majority of their staff is nonprofessional. The majority of libraries provide only basic information services. Cooperation among libraries is limited. Survey results also indicate that a significant number of health sciences libraries are not automated. Some recommendations for the improvement of existing resources, facilities, and services are made. [Abstract/Link to Full Text]

Grodzinski A
A medical book collection for physician assistants.
Bull Med Libr Assoc. 2001 Jul;89(3):277-86.
Selecting resources for physician assistants is challenging and can be overwhelming. Although several core lists exist for nursing, allied health, and medical libraries, judging the scope and level of these resources in relation to the information needs of the physician assistant is difficult. Medical texts can be highly specialized and very expensive, in essence, "overkill" for the needs of the physician assistant. This bibliography is meant to serve as a guide to appropriate medical texts for physician assistants. Titles were selected from the Brandon/Hill list, Doody's Electronic Journal, and various other reference resources. Resources were evaluated based on the subject and scope, audience, authorship, cost, and currency. The collection includes 195 titles from 33 specialty areas. Standard texts in each area are also included. [Abstract/Link to Full Text]

Gluck JC, Hassig RA
Raising the bar: the importance of hospital library standards in the continuing medical education accreditation process.
Bull Med Libr Assoc. 2001 Jul;89(3):272-6.
The Connecticut State Medical Society (CSMS) reviews and accredits the continuing medical education (CME) programs offered by Connecticut's hospitals. As part of the survey process, the CSMS assesses the quality of the hospitals' libraries. In 1987, the CSMS adopted the Medical Library Association's (MLA's) "Minimum Standards for Health Sciences Libraries in Hospitals." In 1990, professional librarians were added to the survey team and, later, to the CSMS CME Committee. Librarians participating in this effort are recruited from the membership of the Connecticut Association of Health Sciences Librarians (CAHSL). The positive results of having a qualified librarian on the survey team and the invaluable impact of adherence to the MLA standards are outlined. As a direct result of this process, hospitals throughout the state have added staffing, increased space, and added funding for resources during an era of cutbacks. Some hospital libraries have been able to maintain a healthy status quo, while others have had proposed cuts reconsidered by administrators for fear of losing valuable CME accreditation status. Creating a relationship with an accrediting agency is one method by which hospital librarians elsewhere may strengthen their efforts to ensure adequate library resources in an era of downsizing. In addition, this collaboration has provided a new and important role for librarians to play on an accreditation team. [Abstract/Link to Full Text]

Paden SL, Batson AL, Wallace RL
Web-based Loansome Doc, librarians, and end users: results from a survey of the Southeast Region.
Bull Med Libr Assoc. 2001 Jul;89(3):263-71.
OBJECTIVES: The study examines how Loansome Doc services are implemented and used by libraries in the Southeast Region and describe end users' experiences with and attitudes toward Loansome Doc. METHODS: 251 active DOCLINE libraries and 867 Loansome Doc users were surveyed. RESULTS: Roughly one half of the libraries offered Loansome Doc services. Of those that did not, most indicated no plans to offer it in the future. The majority had a small number of end users and experienced minimal increases in interlibrary loan activity. Problems were relatively rare. Satisfaction with Loansome Doc was high among all types of libraries. End users were usually physicians or other health care professionals who requested articles for research and patient care. Most learned about Loansome Doc through PubMed or Internet Grateful Med. End users appeared to be largely self-taught or received informal instruction in Loansome Doc. Loansome Doc filled document requests in a timely manner, and end users reported being satisfied with the service. CONCLUSIONS: Greater promotion of what Loansome Doc is and how it can benefit libraries can increase the number of participating libraries. While satisfaction of Loansome Doc end users is high, satisfaction could be increased with more help on the PubMed screen, more library training, and faster delivery methods. [Abstract/Link to Full Text]

Light J, Chapple-Sokol A
More on Loansome Doc.
J Med Libr Assoc. 2002 Jan;90(1):111. [Abstract/Link to Full Text]

Weise FO, McMullen TD
Study to assess the compensation and skills of medical library professionals relative to information technology professionals.
Bull Med Libr Assoc. 2001 Jul;89(3):249-62.
PURPOSE: The study seeks to determine how medical library professionals performing information-technology (IT) roles are compensated and how their positions are designed compared to information technology staff in their institutions. METHODS: 550 medical library directors in hospital and academic medical libraries were surveyed. The data was then compared to survey data from other compensation studies of the IT industry. RESULTS: There is a gap in compensation between medical library professionals and IT professionals performing similar functions using information technology. Technology-intense library jobs are compensated at higher levels than more traditional jobs. CONCLUSIONS: To compete with IT salaries, managers of medical library professionals will need to be ever more cognizant of the employment practices of IT professionals in nonmedical library disciplines. It is typically in the medical library's best interest to ensure that IT-related jobs, accountabilities, and capabilities of the medical library are known and understood by others, especially in the human resources and information technology staff departments. [Abstract/Link to Full Text]

Lipscomb CE
SUNY Biomedical Communication Network: Irwin Pizer.
Bull Med Libr Assoc. 2001 Apr;89(2):231-4. [Abstract/Link to Full Text]

Plutchak TS
One, two, three....
Bull Med Libr Assoc. 2001 Apr;89(2):227-9. [Abstract/Link to Full Text]

Benjes CM, Brown JF
Database-generated Web pages: the Norris Medical Library experience.
Bull Med Libr Assoc. 2001 Apr;89(2):222-4. [Abstract/Link to Full Text]

Flannery MA
Building a retrospective collection in pharmacy: a brief history of the literature with some considerations for U.S. health sciences library professionals.
Bull Med Libr Assoc. 2001 Apr;89(2):212-21.
This paper argues that historical works in pharmacy are important tools for the clinician as well as the historian. With this as its operative premise, delineating the tripartite aspects of pharmacy as a business enterprise, a science, and a profession provides a conceptual framework for primary and secondary resource collecting. A brief history and guide to those materials most essential to a historical collection in pharmacy follows. Issues such as availability and cost are discussed and summarized in checklist form. In addition, a glossary of important terms is provided as well as a list of all the major U.S. dispensatories and their various editions. This paper is intended to serve as a resource for those interested in collecting historical materials in pharmacy and pharmaco-therapeutics as well as provide a history that gives context to these classics in the field. This should provide a rationale for selective retrospective collection development in pharmacy. [Abstract/Link to Full Text]

Ludwig L, Shedlock J, Watson L, Dahlen K, Jenkins C
Designing a library: everyone on the same page?
Bull Med Libr Assoc. 2001 Apr;89(2):204-11.
Excerpts are presented from an interview by the Bulletin of the Medical Library Association buildings projects editor with four academic health sciences library directors: one who had recently completed a major library building project and three who were involved in various stages of new building projects. They share their experiences planning for and implementing library-building programs. The interview explores driving forces leading to new library buildings, identifies who should be involved, recalls the most difficult and exciting moments of the building projects, relates what they wished they had known before starting the project, assesses the impact of new library facilities on clients and services, reviews what they would change, and describes forces impacting libraries today and attributes of the twenty-first century library. [Abstract/Link to Full Text]

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

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

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

Recent Articles in Journal of the American Medical Informatics Association

Kaushal R, Jha AK, Franz C, Glaser J, Shetty KD, Jaggi T, Middleton B, Kuperman GJ, Khorasani R, Tanasijevic M, Bates DW
Return on investment for a computerized physician order entry system.
J Am Med Inform Assoc. 2006 May-Jun;13(3):261-6.
OBJECTIVE: Although computerized physician order entry (CPOE) may decrease errors and improve quality, hospital adoption has been slow. The high costs and limited data on financial benefits of CPOE systems are a major barrier to adoption. The authors assessed the costs and financial benefits of the CPOE system at Brigham and Women's Hospital over ten years. DESIGN: Cost and benefit estimates of a hospital CPOE system at Brigham and Women's Hospital (BWH), a 720-adult bed, tertiary care, academic hospital in Boston. MEASUREMENTS: Institutional experts provided data about the costs of the CPOE system. Benefits were determined from published studies of the BWH CPOE system, interviews with hospital experts, and relevant internal documents. Net overall savings to the institution and operating budget savings were determined. All data are presented as value figures represented in 2002 dollars. RESULTS: Between 1993 and 2002, the BWH spent $11.8 million to develop, implement, and operate CPOE. Over ten years, the system saved BWH $28.5 million for cumulative net savings of $16.7 million and net operating budget savings of $9.5 million given the institutional 80% prospective reimbursement rate. The CPOE system elements that resulted in the greatest cumulative savings were renal dosing guidance, nursing time utilization, specific drug guidance, and adverse drug event prevention. The CPOE system at BWH has resulted in substantial savings, including operating budget savings, to the institution over ten years. CONCLUSION: Other hospitals may be able to save money and improve patient safety by investing in CPOE systems. [Abstract/Link to Full Text]

Ozdas A, Speroff T, Waitman LR, Ozbolt J, Butler J, Miller RA
Integrating "best of care" protocols into clinicians' workflow via care provider order entry: impact on quality-of-care indicators for acute myocardial infarction.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):188-96.
OBJECTIVE: In the context of an inpatient care provider order entry (CPOE) system, to evaluate the impact of a decision support tool on integration of cardiology "best of care" order sets into clinicians' admission workflow, and on quality measures for the management of acute myocardial infarction (AMI) patients. DESIGN: A before-and-after study of physician orders evaluated (1) per-patient use rates of standardized acute coronary syndrome (ACS) order set and (2) patient-level compliance with two individual recommendations: early aspirin ordering and beta-blocker ordering. MEASUREMENTS: The effectiveness of the intervention was evaluated for (1) all patients with ACS (suspected for AMI at the time of admission) (N = 540) and (2) the subset of the ACS patients with confirmed discharge diagnosis of AMI (n = 180) who comprise the recommended target population who should receive aspirin and/or beta-blockers. Compliance rates for use of the ACS order set, aspirin ordering, and beta-blocker ordering were calculated as the percentages of patients who had each action performed within 24 hours of admission. RESULTS: For all ACS admissions, the decision support tool significantly increased use of the ACS order set (p = 0.009). Use of the ACS order set led, within the first 24 hours of hospitalization, to a significant increase in the number of patients who received aspirin (p = 0.001) and a nonsignificant increase in the number of patients who received beta-blockers (p = 0.07). Results for confirmed AMI cases demonstrated similar increases, but did not reach statistical significance. CONCLUSION: The decision support tool increased optional use of the ACS order set, but room for additional improvement exists. [Abstract/Link to Full Text]

Corby PM, Schleyer T, Spallek H, Hart TC, Weyant RJ, Corby AL, Bretz WA
Using biometrics for participant identification in a research study: a case report.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):233-5.
This paper illustrates the use of biometrics through the application of an iris-based biometrics system for identifying twins and their parents in a longitudinal research study. It explores the use of biometrics (science of measuring physical or anatomical characteristics of individuals) as a technology for correct identification of individuals during longitudinal studies to help ensure data fidelity. Examples of these circumstances include longitudinal epidemiological and genetic studies, clinical trials, and multicenter collaborative studies where accurate identification of subjects over time can be difficult when the subject may be young or an unreliable source of identification information. The use of technology can automate the process of subject identification thereby reducing the need to depend on subject recall during repeated visits thus helping to ensure data quality. This case report provides insights that may serve as useful hints for those responsible for planning system implementation that involves participants' authentication that would require a more secure form of identification. [Abstract/Link to Full Text]

van der Sijs H, Aarts J, Vulto A, Berg M
Overriding of drug safety alerts in computerized physician order entry.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):138-47.
Many computerized physician order entry (CPOE) systems have integrated drug safety alerts. The authors reviewed the literature on physician response to drug safety alerts and interpreted the results using Reason's framework of accident causation. In total, 17 papers met the inclusion criteria. Drug safety alerts are overridden by clinicians in 49% to 96% of cases. Alert overriding may often be justified and adverse drug events due to overridden alerts are not always preventable. A distinction between appropriate and useful alerts should be made. The alerting system may contain error-producing conditions like low specificity, low sensitivity, unclear information content, unnecessary workflow disruptions, and unsafe and inefficient handling. These may result in active failures of the physician, like ignoring alerts, misinterpretation, and incorrect handling. Efforts to improve patient safety by increasing correct handling of drug safety alerts should focus on the error-producing conditions in software and organization. Studies on cognitive processes playing a role in overriding drug safety alerts are lacking. [Abstract/Link to Full Text]

Tamblyn R, Huang A, Kawasumi Y, Bartlett G, Grad R, Jacques A, Dawes M, Abrahamowicz M, Perreault R, Taylor L, Winslade N, Poissant L, Pinsonneault A
The development and evaluation of an integrated electronic prescribing and drug management system for primary care.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):148-59.
OBJECTIVE: To develop and evaluate the acceptability and use of an integrated electronic prescribing and drug management system (MOXXI) for primary care physicians. DESIGN: A 20-month follow-up study of MOXXI (Medical Office of the XXIst Century) implementation in 28 primary care physicians and 13,515 consenting patients. MEASUREMENT: MOXXI was developed to enhance patient safety by integrating patient demographics, retrieving active drugs from pharmacy systems, generating an automated problem list, and providing electronic prescription, stop order, automated prescribing problem alerts, and compliance monitoring functions. Evaluation of technical performance, acceptability, and use was conducted using audit trails, questionnaires, standardized tasks, and information from comprehensive health insurance databases. RESULTS: Perceived improvements in continuity of care and professional autonomy were associated with physicians' expected use of MOXXI. Physician speed in using MOXXI improved substantially in the first three months; however, only the represcribing function was faster using MOXXI than by handwritten prescription. Physicians wrote electronic prescriptions in 36.9 per 100 visits and reviewed the patient's drug profile in 12.6 per 100 visits. Physicians rated printed prescriptions, the current drug list, and the represcribing function as the most beneficial aspects of the system. Physicians were more likely to use the drug profile for patients who used more medication, made more emergency department visits, had more prescribing physicians, and lower continuity of care. CONCLUSION: Primary care physicians believed an integrated electronic prescribing and drug management system would improve continuity of care, and they were more likely to use the system for patients with more complex, fragmented care. [Abstract/Link to Full Text]

Matheny ME, Ohno-Machado L, Resnic FS
Monitoring device safety in interventional cardiology.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):180-7.
OBJECTIVE: A variety of postmarketing surveillance strategies to monitor the safety of medical devices have been supported by the U.S. Food and Drug Administration, but there are few systems to automate surveillance. Our objective was to develop a system to perform real-time monitoring of safety data using a variety of process control techniques. DESIGN: The Web-based Data Extraction and Longitudinal Time Analysis (DELTA) system imports clinical data in real-time from an electronic database and generates alerts for potentially unsafe devices or procedures. The statistical techniques used are statistical process control (SPC), logistic regression (LR), and Bayesian updating statistics (BUS). MEASUREMENTS: We selected in-patient mortality following implantation of the Cypher drug-eluting coronary stent to evaluate our system. Data from the University of Michigan Consortium Bare-Metal Stent Study was used to calculate the event rate alerting boundaries. Data analysis was performed on local catheterization data from Brigham and Women's Hospital from July 1, 2003, shortly after the Cypher release, to December 31, 2004, including 2,270 cases with 27 observed deaths. RESULTS: The single-stratum SPC had alerts in months 4 and 10. The multistrata SPC had alerts in months 5, 10, and 18 in the moderate-risk stratum, and months 1, 4, 7, and 10 in the high-risk stratum. The only cumulative alerts were in the first month for the high-risk stratum of the multistrata SPC. The LR method showed no monthly or cumulative alerts. The BUS method showed an alert in the first month for the high-risk stratum. CONCLUSION: The system performed adequately within the Brigham and Women's Hospital Intranet environment based on the design goals. All three cumulative methods agreed that the overall observed event rates were not significantly higher for the new medical device than for a closely related medical device and were consistent with the observation that the initial concerns about this device dissipated as more data accumulated. [Abstract/Link to Full Text]

Dinakarpandian D, Lee Y, Vishwanath K, Lingambhotla R
MachineProse: an ontological framework for scientific assertions.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):220-32.
OBJECTIVE: The idea of testing a hypothesis is central to the practice of biomedical research. However, the results of testing a hypothesis are published mainly in the form of prose articles. Encoding the results as scientific assertions that are both human and machine readable would greatly enhance the synergistic growth and dissemination of knowledge. DESIGN: We have developed MachineProse (MP), an ontological framework for the concise specification of scientific assertions. MP is based on the idea of an assertion constituting a fundamental unit of knowledge. This is in contrast to current approaches that use discrete concept terms from domain ontologies for annotation and assertions are only inferred heuristically. MEASUREMENTS: We use illustrative examples to highlight the advantages of MP over the use of the Medical Subject Headings (MeSH) system and keywords in indexing scientific articles. RESULTS: We show how MP makes it possible to carry out semantic annotation of publications that is machine readable and allows for precise search capabilities. In addition, when used by itself, MP serves as a knowledge repository for emerging discoveries. A prototype for proof of concept has been developed that demonstrates the feasibility and novel benefits of MP. As part of the MP framework, we have created an ontology of relationship types with about 100 terms optimized for the representation of scientific assertions. CONCLUSION: MachineProse is a novel semantic framework that we believe may be used to summarize research findings, annotate biomedical publications, and support sophisticated searches. [Abstract/Link to Full Text]

Hersh W
Who are the informaticians? What we know and should know.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):166-70.
The beginning of the 21st century has seen a surge in interest and enthusiasm for health care information technology based on its ability to demonstrate improvements in the quality, safety, and cost-efficiency of health care. One question, however, for which we have fewer answers is "who will be the individuals that develop, implement, and evaluate these systems?" In particular, while most attention has been paid to the exemplar leaders in health information technology, less has been focused on the issue of the workforce necessary to sustain the systems to achieve their vision. The discipline of medical informatics must pay sufficient attention to the professional workforce that will deploy systems outside the informatics research setting so their benefits may more widely accrue. [Abstract/Link to Full Text]

Cassa CA, Grannis SJ, Overhage JM, Mandl KD
A context-sensitive approach to anonymizing spatial surveillance data: impact on outbreak detection.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):160-5.
OBJECTIVE: The use of spatially based methods and algorithms in epidemiology and surveillance presents privacy challenges for researchers and public health agencies. We describe a novel method for anonymizing individuals in public health data sets by transposing their spatial locations through a process informed by the underlying population density. Further, we measure the impact of the skew on detection of spatial clustering as measured by a spatial scanning statistic. DESIGN: Cases were emergency department (ED) visits for respiratory illness. Baseline ED visit data were injected with artificially created clusters ranging in magnitude, shape, and location. The geocoded locations were then transformed using a de-identification algorithm that accounts for the local underlying population density. MEASUREMENTS: A total of 12,600 separate weeks of case data with artificially created clusters were combined with control data and the impact on detection of spatial clustering identified by a spatial scan statistic was measured. RESULTS: The anonymization algorithm produced an expected skew of cases that resulted in high values of data set k-anonymity. De-identification that moves points an average distance of 0.25 km lowers the spatial cluster detection sensitivity by less than 4% and lowers the detection specificity less than 1%. CONCLUSION: A population-density-based Gaussian spatial blurring markedly decreases the ability to identify individuals in a data set while only slightly decreasing the performance of a standardly used outbreak detection tool. These findings suggest new approaches to anonymizing data for spatial epidemiology and surveillance. [Abstract/Link to Full Text]

Cohen AM, Hersh WR, Peterson K, Yen PY
Reducing workload in systematic review preparation using automated citation classification.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):206-19.
OBJECTIVE: To determine whether automated classification of document citations can be useful in reducing the time spent by experts reviewing journal articles for inclusion in updating systematic reviews of drug class efficacy for treatment of disease. DESIGN: A test collection was built using the annotated reference files from 15 systematic drug class reviews. A voting perceptron-based automated citation classification system was constructed to classify each article as containing high-quality, drug class-specific evidence or not. Cross-validation experiments were performed to evaluate performance. MEASUREMENTS: Precision, recall, and F-measure were evaluated at a range of sample weightings. Work saved over sampling at 95% recall was used as the measure of value to the review process. RESULTS: A reduction in the number of articles needing manual review was found for 11 of the 15 drug review topics studied. For three of the topics, the reduction was 50% or greater. CONCLUSION: Automated document citation classification could be a useful tool in maintaining systematic reviews of the efficacy of drug therapy. Further work is needed to refine the classification system and determine the best manner to integrate the system into the production of systematic reviews. [Abstract/Link to Full Text]

Par� G, Sicotte C, Jacques H
The effects of creating psychological ownership on physicians' acceptance of clinical information systems.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):197-205.
OBJECTIVE: Motivated by the need to push further our understanding of physicians' acceptance of clinical information systems, we propose a relatively new construct, namely, psychological ownership. We situated the construct within a nomological net using a prevailing and dominant information technology adoption behavior model as a logical starting point. DESIGN: A mail survey was sent to the population of users of a regional physician order entry (POE) system aimed at speeding up the transmission of clinical data, mainly laboratory tests and radiology examinations, within a community health network. MEASUREMENTS: All scales, but one, were measured using previously validated instruments. For its part, the psychological ownership scale was developed using a multistage iterative procedure. RESULTS: Ninety-one questionnaires were returned to the researchers, for a response rate of 72.8%. Our findings reveal that, in order to foster physicians' adoption of a clinical information system, it is important to encourage and cultivate a positive attitude toward using the new system. In this connection, positive perception of the technology's usefulness is crucial. Second, results demonstrate that psychological ownership of a POE system is positively associated with physicians' perceptions of system utility and system user friendliness. Last, through their active involvement and participation, physicians feel they have greater influence on the development process, thereby developing feelings of ownership toward the clinical system. CONCLUSION: Psychological ownership's highly significant associations with user participation and crucial beliefs driving technology acceptance behaviors among physicians affirm the value of this construct in extending our understanding of POE adoption. [Abstract/Link to Full Text]

Berner ES, Houston TK, Ray MN, Allison JJ, Heudebert GR, Chatham WW, Kennedy JI, Glandon GL, Norton PA, Crawford MA, Maisiak RS
Improving ambulatory prescribing safety with a handheld decision support system: a randomized controlled trial.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):171-9.
OBJECTIVE: To evaluate the effectiveness of a personal digital assistant (PDA)-based clinical decision support system (CDSS) on nonsteroidal anti-inflammatory drug (NSAID) prescribing safety in the outpatient setting. DESIGN: The design was a randomized, controlled trial conducted in a university-based resident clinic. Internal medicine residents received a PDA-based CDSS suite. For intervention residents, the CDSS included a prediction rule for NSAID-related gastrointestinal risk assessment and treatment recommendations. Unannounced standardized patients (SPs) trained to portray musculoskeletal symptoms presented to study physicians. Safety outcomes were assessed from the prescriptions given to the SPs. Each prescription was reviewed by a committee of clinicians blinded to participant, intervention group assignment, and baseline or follow-up status. MEASUREMENTS: Prescriptions were judged as safe or unsafe. The main outcome measure was the differential change in unsafe prescribing of NSAIDs for the intervention versus the control group. RESULTS: At baseline, the mean proportion of cases per physician with unsafe prescriptions for the two groups was similar (0.27 vs. 0.29, p > 0.05). Controlling for baseline performance, intervention participants prescribed more safely than controls after receiving the CDSS (0.23 vs. 0.45 [F = 4.24, p < 0.05]). With the CDSS, intervention participants documented more complete assessment of patient gastrointestinal risk from NSAIDs. CONCLUSION: PARTICIPANTS provided with a PDA-based CDSS for NSAID prescribing made fewer unsafe treatment decisions than participants without the CDSS. [Abstract/Link to Full Text]

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

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

Barnett GO
Report to the National Institutes of Health Division of Research Grants Computer Research Study Section on computer applications in medical communication and information retrieval systems as related to the improvement of patient care and the medical record--September 26, 1966.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):127-35; discussion 136-7. [Abstract/Link to Full Text]

Lindberg DA
Commentary on G. Octo Barnett's Report to the Computer Research Study Section.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):136-7. [Abstract/Link to Full Text]

Tang PC, Ash JS, Bates DW, Overhage JM, Sands DZ
Personal health records: definitions, benefits, and strategies for overcoming barriers to adoption.
J Am Med Inform Assoc. 2006 Mar-Apr;13(2):121-6.
Recently there has been a remarkable upsurge in activity surrounding the adoption of personal health record (PHR) systems for patients and consumers. The biomedical literature does not yet adequately describe the potential capabilities and utility of PHR systems. In addition, the lack of a proven business case for widespread deployment hinders PHR adoption. In a 2005 working symposium, the American Medical Informatics Association's College of Medical Informatics discussed the issues surrounding personal health record systems and developed recommendations for PHR-promoting activities. Personal health record systems are more than just static repositories for patient data; they combine data, knowledge, and software tools, which help patients to become active participants in their own care. When PHRs are integrated with electronic health record systems, they provide greater benefits than would stand-alone systems for consumers. This paper summarizes the College Symposium discussions on PHR systems and provides definitions, system characteristics, technical architectures, benefits, barriers to adoption, and strategies for increasing adoption. [Abstract/Link to Full Text]

Zeng QT, Tse T
Exploring and developing consumer health vocabularies.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):24-9.
Laypersons ("consumers") often have difficulty finding, understanding, and acting on health information due to gaps in their domain knowledge. Ideally, consumer health vocabularies (CHVs) would reflect the different ways consumers express and think about health topics, helping to bridge this vocabulary gap. However, despite the recent research on mismatches between consumer and professional language (e.g., lexical, semantic, and explanatory), there have been few systematic efforts to develop and evaluate CHVs. This paper presents the point of view that CHV development is practical and necessary for extending research on informatics-based tools to facilitate consumer health information seeking, retrieval, and understanding. In support of the view, we briefly describe a distributed, bottom-up approach for (1) exploring the relationship between common consumer health expressions and professional concepts and (2) developing an open-access, preliminary (draft) "first-generation" CHV. While recognizing the limitations of the approach (e.g., not addressing psychosocial and cultural factors), we suggest that such exploratory research and development will yield insights into the nature of consumer health expressions and assist developers in creating tools and applications to support consumer health information seeking. [Abstract/Link to Full Text]

Linder JA, Bates DW, Williams DH, Connolly MA, Middleton B
Acute infections in primary care: accuracy of electronic diagnoses and electronic antibiotic prescribing.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):61-6.
OBJECTIVE: To maximize effectiveness, clinical decision-support systems must have access to accurate diagnostic and prescribing information. We measured the accuracy of electronic claims diagnoses and electronic antibiotic prescribing for acute respiratory infections (ARIs) and urinary tract infections (UTIs) in primary care. DESIGN: A retrospective, cross-sectional study of randomly selected visits to nine clinics in the Brigham and Women's Practice-Based Research Network between 2000 and 2003 with a principal claims diagnosis of an ARI or UTI (N = 827). MEASUREMENTS: We compared electronic billing diagnoses and electronic antibiotic prescribing to the gold standard of blinded chart review. RESULTS: Claims-derived, electronic ARI diagnoses had a sensitivity of 98%, specificity of 96%, and positive predictive value of 96%. Claims-derived, electronic UTI diagnoses had a sensitivity of 100%, specificity of 87%, and positive predictive value of 85%. According to the visit note, physicians prescribed antibiotics in 45% of ARI visits and 73% of UTI visits. Electronic antibiotic prescribing had a sensitivity of 43%, specificity of 93%, positive predictive value of 90%, and simple agreement of 64%. The sensitivity of electronic antibiotic prescribing increased over time from 22% in 2000 to 58% in 2003 (p for trend < 0.0001). CONCLUSION: Claims-derived, electronic diagnoses for ARIs and UTIs appear accurate. Although closing, a large gap persists between antibiotic prescribing documented in the visit note and the use of electronic antibiotic prescribing. Barriers to electronic antibiotic prescribing in primary care must be addressed to leverage the potential that computerized decision-support systems offer in reducing costs, improving quality, and improving patient safety. [Abstract/Link to Full Text]

Staes CJ, Bennett ST, Evans RS, Narus SP, Huff SM, Sorensen JB
A case for manual entry of structured, coded laboratory data from multiple sources into an ambulatory electronic health record.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):12-5.
Laboratory results provide necessary information for the management of ambulatory patients. To realize the benefits of an electronic health record (EHR) and coded laboratory data (e.g., decision support and improved data access and display), results from laboratories that are external to the health care enterprise need to be integrated with internal results. We describe the development and clinical impact of integrating external results into the EHR at Intermountain Health Care (IHC). During 2004, over 14,000 external laboratory results for 128 liver transplant patients were added to the EHR. The results were used to generate computerized alerts that assisted clinicians with managing laboratory tests in the ambulatory setting. The external results were sent from 85 different facilities and can now be viewed in the EHR integrated with IHC results. We encountered regulatory, logistic, economic, and data quality issues that should be of interest to others developing similar applications. [Abstract/Link to Full Text]

Loonsk JW, McGarvey SR, Conn LA, Johnson J
The Public Health Information Network (PHIN) Preparedness initiative.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):1-4.
The Public Health Information Network (PHIN) Preparedness initiative strives to implement, on an accelerated pace, a consistent national network of information systems that will support public health in being prepared for public health emergencies. Using the principles and practices of the broader PHIN initiative, PHIN Preparedness concentrates in the short term on ensuring that all public health jurisdictions have, or have access to, systems to accomplish known preparedness functions. The PHIN Preparedness initiative defines functional requirements, technical standards and specifications, and a process to achieve consistency and interconnectedness of preparedness systems across public health. [Abstract/Link to Full Text]

Zeng QT, Crowell J, Plovnick RM, Kim E, Ngo L, Dibble E
Assisting consumer health information retrieval with query recommendations.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):80-90.
OBJECTIVE: Health information retrieval (HIR) on the Internet has become an important practice for millions of people, many of whom have problems forming effective queries. We have developed and evaluated a tool to assist people in health-related query formation. DESIGN: We developed the Health Information Query Assistant (HIQuA) system. The system suggests alternative/additional query terms related to the user's initial query that can be used as building blocks to construct a better, more specific query. The recommended terms are selected according to their semantic distance from the original query, which is calculated on the basis of concept co-occurrences in medical literature and log data as well as semantic relations in medical vocabularies. MEASUREMENTS: An evaluation of the HIQuA system was conducted and a total of 213 subjects participated in the study. The subjects were randomized into 2 groups. One group was given query recommendations and the other was not. Each subject performed HIR for both a predefined and a self-defined task. RESULTS: The study showed that providing HIQuA recommendations resulted in statistically significantly higher rates of successful queries (odds ratio = 1.66, 95% confidence interval = 1.16-2.38), although no statistically significant impact on user satisfaction or the users' ability to accomplish the predefined retrieval task was found. CONCLUSION: Providing semantic-distance-based query recommendations can help consumers with query formation during HIR. [Abstract/Link to Full Text]

Weingart SN, Rind D, Tofias Z, Sands DZ
Who uses the patient internet portal? The PatientSite experience.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):91-5.
OBJECTIVE: Although the patient Internet portal is a potentially transformative technology, there is little scientific information about the demographic and clinical characteristics of portal enrollees and the features that they access. DESIGN: We describe two pilot studies of a comprehensive Internet portal called PatientSite. These pilots include a prospective one-year cohort study of all patients who enrolled in April 2003 and a case-control study in 2004 of enrollees and nonenrollees at two hospital-based primary care practices. MEASUREMENTS: The cohort study tracked patient enrollment and features in PatientSite that enrollees accessed, such as laboratory and radiology results, prescription renewals, appointment requests, managed care referrals, and clinical messaging. The case-control study used medical record review to compare the demographic and clinical characteristics of 100 randomly selected PatientSite enrollees and 100 nonenrollees. RESULTS: PatientSite use grew steadily after its introduction. New enrollees logged in most frequently in the first month, but 26% to 77% of the cohort continued to access the portal at least monthly. They most often examined laboratory and radiology results and sent clinical messages to their providers. PatientSite enrollees were younger and more affluent and had fewer medical problems than nonenrollees. CONCLUSION: Expanding the use of patient portals will require an understanding of obstacles that prevent access for those who might benefit most from this technology. [Abstract/Link to Full Text]

Podichetty VK, Varley E
e-Talking to patients: connecting with the health care consumer.
J Am Med Inform Assoc. 2006 Sep-Oct;13(5):579; author reply 580. [Abstract/Link to Full Text]

Maviglia SM, Yoon CS, Bates DW, Kuperman G
KnowledgeLink: impact of context-sensitive information retrieval on clinicians' information needs.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):67-73.
OBJECTIVE: Infobuttons are message-based content search and retrieval functions embedded within other applications that dynamically return information relevant to the clinical task at hand. The objective of this study was to determine whether infobuttons effectively answer providers' questions about medications or affect patient care decisions. DESIGN: The authors implemented and evaluated a medication infobutton application called KnowledgeLink. Health care providers at 18 outpatient clinics were randomized to one of two versions of KnowledgeLink, one that linked to information from Micromedex (Thomson Micromedex, Greenwood Village, Co) and the other to material from SkolarMD (Wolters Kluwer Health, Palo Alto, CA). MEASUREMENTS: Data were collected about the frequency of use and demographics of users, patients, and drugs that were queried. Users were periodically surveyed with short questionnaires and then with a more extensive survey at the end of one year. RESULTS: During the first year, KnowledgeLink was used 7,972 times by 359 users to look up information about 1,723 medications for 4,961 patients. Clinicians used KnowledgeLink twice a month on average, and during an average of 1.2% of patient encounters. KnowledgeLink was used by a wide variety of medical staff, not just physicians and nurse practitioners. The frequency of usage and the questions asked varied with user role (primary care physician, specialist physician, nurse practitioner). Although the median KnowledgeLink session was brief (21 seconds), KnowledgeLink answered users' queries 84% of the time, and altered patient care decisions 15% of the time. Users rated KnowledgeLink favorably on multiple scales, recommended extending KnowledgeLink to other content domains, and suggested enhancing the interface to allow refinement of the query and selection of the target resource. CONCLUSION: An infobutton can satisfy information needs about medications. Although used infrequently and for brief sessions, KnowledgeLink was positively received, answered most users' questions, and had a significant impact on medical decision making. The next steps would be to broaden the domains that KnowledgeLink covers to more specifically tailor results to the user type, to provide options when queries are not immediately answered, and to implement KnowledgeLink within other electronic clinical applications. [Abstract/Link to Full Text]

Shah NR, Seger AC, Seger DL, Fiskio JM, Kuperman GJ, Blumenfeld B, Recklet EG, Bates DW, Gandhi TK
Improving acceptance of computerized prescribing alerts in ambulatory care.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):5-11.
Computerized drug prescribing alerts can improve patient safety, but are often overridden because of poor specificity and alert overload. Our objective was to improve clinician acceptance of drug alerts by designing a selective set of drug alerts for the ambulatory care setting and minimizing workflow disruptions by designating only critical to high-severity alerts to be interruptive to clinician workflow. The alerts were presented to clinicians using computerized prescribing within an electronic medical record in 31 Boston-area practices. There were 18,115 drug alerts generated during our six-month study period. Of these, 12,933 (71%) were noninterruptive and 5,182 (29%) interruptive. Of the 5,182 interruptive alerts, 67% were accepted. Reasons for overrides varied for each drug alert category and provided potentially useful information for future alert improvement. These data suggest that it is possible to design computerized prescribing decision support with high rates of alert recommendation acceptance by clinicians. [Abstract/Link to Full Text]

Lasko TA, Atlas SJ, Barry MJ, Chueh HC
Automated identification of a physician's primary patients.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):74-9.
OBJECTIVE: To develop and validate an automated method for determining the set of patients for whom a given primary care physician holds overall clinical responsibility. DESIGN: The study included all adult patients (16,185) seen at least once in an ambulatory setting during a three-year period by 18 primary care physicians in ten practices. The physicians indicated whether they considered themselves to be the physician primarily responsible for the overall clinical care of each visiting patient. Statistical models were constructed to predict the physicians' designations using predictor variables derived from electronically available appointment schedules and demographic information. MEASUREMENTS: Predictive accuracy was assessed primarily using the area under the receiver-operating characteristic curve (AUC), and secondarily using positive predictive value (PPV) and sensitivity. RESULTS: A minimal set of six variables was identified as predictive of the physicians' designations. The constructed model had a median AUC for individual physicians of 0.92 (interquartile interval: 0.90-0.96), a PPV of 0.94 (interquartile interval: 0.87-0.95), and a sensitivity of 0.95 (interquartile interval: 0.87-0.97). CONCLUSION: A statistical model using a minimal set of commonly available electronic data can accurately predict the set of patients for whom a physician holds primary clinical responsibility. Further research examining the generalization of the model to other settings would be valuable. [Abstract/Link to Full Text]

Dolin RH, Alschuler L, Boyer S, Beebe C, Behlen FM, Biron PV, Shabo Shvo A
HL7 Clinical Document Architecture, Release 2.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):30-9.
Clinical Document Architecture, Release One (CDA R1), became an American National Standards Institute (ANSI)-approved HL7 Standard in November 2000, representing the first specification derived from the Health Level 7 (HL7) Reference Information Model (RIM). CDA, Release Two (CDA R2), became an ANSI-approved HL7 Standard in May 2005 and is the subject of this article, where the focus is primarily on how the standard has evolved since CDA R1, particularly in the area of semantic representation of clinical events. CDA is a document markup standard that specifies the structure and semantics of a clinical document (such as a discharge summary or progress note) for the purpose of exchange. A CDA document is a defined and complete information object that can include text, images, sounds, and other multimedia content. It can be transferred within a message and can exist independently, outside the transferring message. CDA documents are encoded in Extensible Markup Language (XML), and they derive their machine processable meaning from the RIM, coupled with terminology. The CDA R2 model is richly expressive, enabling the formal representation of clinical statements (such as observations, medication administrations, and adverse events) such that they can be interpreted and acted upon by a computer. On the other hand, CDA R2 offers a low bar for adoption, providing a mechanism for simply wrapping a non-XML document with the CDA header or for creating a document with a structured header and sections containing only narrative content. The intent is to facilitate widespread adoption, while providing a mechanism for incremental semantic interoperability. [Abstract/Link to Full Text]

Bernstam EV, Herskovic JR, Aphinyanaphongs Y, Aliferis CF, Sriram MG, Hersh WR
Using citation data to improve retrieval from MEDLINE.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):96-105.
OBJECTIVE: To determine whether algorithms developed for the World Wide Web can be applied to the biomedical literature in order to identify articles that are important as well as relevant. DESIGN AND MEASUREMENTS A direct comparison of eight algorithms: simple PubMed queries, clinical queries (sensitive and specific versions), vector cosine comparison, citation count, journal impact factor, PageRank, and machine learning based on polynomial support vector machines. The objective was to prioritize important articles, defined as being included in a pre-existing bibliography of important literature in surgical oncology. RESULTS Citation-based algorithms were more effective than noncitation-based algorithms at identifying important articles. The most effective strategies were simple citation count and PageRank, which on average identified over six important articles in the first 100 results compared to 0.85 for the best noncitation-based algorithm (p < 0.001). The authors saw similar differences between citation-based and noncitation-based algorithms at 10, 20, 50, 200, 500, and 1,000 results (p < 0.001). Citation lag affects performance of PageRank more than simple citation count. However, in spite of citation lag, citation-based algorithms remain more effective than noncitation-based algorithms. CONCLUSION Algorithms that have proved successful on the World Wide Web can be applied to biomedical information retrieval. Citation-based algorithms can help identify important articles within large sets of relevant results. Further studies are needed to determine whether citation-based algorithms can effectively meet actual user information needs. [Abstract/Link to Full Text]

Demner-Fushman D, Few B, Hauser SE, Thoma G
Automatically identifying health outcome information in MEDLINE records.
J Am Med Inform Assoc. 2006 Jan-Feb;13(1):52-60.
OBJECTIVE: Understanding the effect of a given intervention on the patient's health outcome is one of the key elements in providing optimal patient care. This study presents a methodology for automatic identification of outcomes-related information in medical text and evaluates its potential in satisfying clinical information needs related to health care outcomes. DESIGN: An annotation scheme based on an evidence-based medicine model for critical appraisal of evidence was developed and used to annotate 633 MEDLINE citations. Textual, structural, and meta-information features essential to outcome identification were learned from the created collection and used to develop an automatic system. Accuracy of automatic outcome identification was assessed in an intrinsic evaluation and in an extrinsic evaluation, in which ranking of MEDLINE search results obtained using PubMed Clinical Queries relied on identified outcome statements. MEASUREMENTS: The accuracy and positive predictive value of outcome identification were calculated. Effectiveness of the outcome-based ranking was measured using mean average precision and precision at rank 10. RESULTS: Automatic outcome identification achieved 88% to 93% accuracy. The positive predictive value of individual sentences identified as outcomes ranged from 30% to 37%. Outcome-based ranking improved retrieval accuracy, tripling mean average precision and achieving 389% improvement in precision at rank 10. CONCLUSION: Preliminary results in outcome-based document ranking show potential validity of the evidence-based medicine-model approach in timely delivery of information critical to clinical decision support at the point of service. [Abstract/Link to Full Text]

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

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

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

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

Recent Articles in Journal of the Medical Library Association

Shisler CM
Evaluating your nursing collection: a quick way to preserve nursing history in a working collection.
J Med Libr Assoc. 2007 Jul;95(3):278-83. [Abstract/Link to Full Text]

Patrick TB, Craven CK, Folk LC
The need for a multidisciplinary team approach to life science workflows.
J Med Libr Assoc. 2007 Jul;95(3):274-8. [Abstract/Link to Full Text]

Sathe NA, Jerome R, Bettinsoli Giuse N
Librarian-perceived barriers to the implementation of the informationist/information specialist in context role.
J Med Libr Assoc. 2007 Jul;95(3):270-4. [Abstract/Link to Full Text]

Hatfield AJ, Kelley SD
Case study: lessons learned through digitizing the National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research Collection.
J Med Libr Assoc. 2007 Jul;95(3):267-70. [Abstract/Link to Full Text]

Rethlefsen ML
Citation analysis of Minnesota Department of Health official publications and journal articles: a needs assessment for the RN Barr Library.
J Med Libr Assoc. 2007 Jul;95(3):260-6.
OBJECTIVE: The paper describes the information needs of a state public health agency, compares needs to its library's collection, and evaluates collection development policy accordingly. METHODS: A citation analysis of journal articles authored by Minnesota Department of Health staff as well as official publications from 2002 to 2004 was conducted. Fifty-six publications fitting the criteria for inclusion in the study were identified using PubMed and library records. Information on each cited reference was recorded, including reference type, relative age of citation, and journal name, if applicable. The library's collection and collection development policies were analyzed in regard to the results. RESULTS: As expected, journals were the most heavily cited format: 63% (n = 897) of all citations were to journal articles. Most cited materials were between 2 and 5 years old. The 897 journal citations represented 265 different journals. The top 10 cited journals (4% of all titles) accounted for 36% (n = 320) of all citations; 62% (n = 320) of journals were cited only once. Of the total journals cited, the library subscribed to 70% (n = 627). DISCUSSION: Overall, no large gaps appeared in the RN Barr Library's journal collection. The analysis confirms that the library's collections budget for serials and books reflects the cited use of these materials. [Abstract/Link to Full Text]

Fenton SH, Badgett RG
A comparison of primary care information content in UpToDate and the National Guideline Clearinghouse.
J Med Libr Assoc. 2007 Jul;95(3):255-9.
OBJECTIVES: The study sought to determine if two major resources for primary care questions have significant differences in information content and whether the number of documents found differs by disease category, patient age, or patient gender. METHODS: Seven hundred fifty-two questions were randomly selected from the Clinical Questions Collection of the National Library of Medicine. UpToDate and the National Guidelines Clearinghouse (NGC) were searched utilizing keywords from the questions. The number of documents retrieved for each question in the resources was recorded. Chi-squared analysis was used to compare differences in retrieval between the resources. Logistic regression was used to evaluate the effect of patient age, patient gender, or disease category on the ability to find content. RESULTS: UpToDate returned 1 or more documents for 580 questions, while NGC returned at least 1 document for 493 questions (77.1% versus 65.5% of question sampled, P = 0.001). In combination, the 2 resources returned content for 91% of searches (n = 685). NGC retrieved a mean of 16.3 documents per question versus 8.7 documents from UpToDate. Disease category was the only variable having a significant impact on the presence of online resource content. CONCLUSIONS: UpToDate had greater breadth of content than NGC, while neither resource provided complete coverage. Current practice guidelines, as reflected by those in the NGC, addressed at most two-thirds of the selected clinical questions. [Abstract/Link to Full Text]

McKibbon KA, Haynes RB, McKinlay RJ, Lokker C
Which journals do primary care physicians and specialists access from an online service?
J Med Libr Assoc. 2007 Jul;95(3):246-54.
OBJECTIVE: The study sought to determine which online journals primary care physicians and specialists not affiliated with an academic medical center access and how the accesses correlate with measures of journal quality and importance. METHODS: Observational study of full-text accesses made during an eighteen-month digital library trial was performed. Access counts were correlated with six methods composed of nine measures for assessing journal importance: ISI impact factors; number of high-quality articles identified during hand-searches of key clinical journals; production data for ACP Journal Club, InfoPOEMs, and Evidence-Based Medicine; and mean clinician-provided clinical relevance and newsworthiness scores for individual journal titles. RESULTS: Full-text journals were accessed 2,322 times by 87 of 105 physicians. Participants accessed 136 of 348 available journal titles. Physicians often selected journals with relatively higher numbers of articles abstracted in ACP Journal Club. Accesses also showed significant correlations with 6 other measures of quality. Specialists' access patterns correlated with 3 measures, with weaker correlations than for primary care physicians. CONCLUSIONS: Primary care physicians, more so than specialists, chose full-text articles from clinical journals deemed important by several measures of value. Most journals accessed by both groups were of high quality as measured by this study's methods for assessing journal importance. [Abstract/Link to Full Text]

Todd PM, Jerome RN, Jarquin-Valdivia AA
Organ preservation in a brain dead patient: information support for neurocritical care protocol development.
J Med Libr Assoc. 2007 Jul;95(3):238-45. [Abstract/Link to Full Text]

Braude RM
Mark E. Funk, AHIP, Medical Library Association President 2007-2008.
J Med Libr Assoc. 2007 Jul;95(3):235-7. [Abstract/Link to Full Text]

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

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

Alpi KM
We are all public health.
J Med Libr Assoc. 2007 Jul;95(3):229-31. [Abstract/Link to Full Text]

Volk RM
Expert searching in consumer health: an important role for librarians in the age of the Internet and the Web.
J Med Libr Assoc. 2007 Apr;95(2):203-7, e66.
OBJECTIVES: The Patient Education Resource Center at the University of Michigan Comprehensive Cancer Center conducts mediated searches for patients and families seeking information on complex medical issues, state-of-the-art treatments, and rare cancers. The current study examined user satisfaction and the impact of information provided to this user population. METHODS: This paper presents the results of 566 user evaluation forms collected between July 2000 and June 2006 (1,532 forms distributed; 37% response rate). Users provided both quantitative and qualitative feedback, which was analyzed and classified into recurrent themes. RESULTS: The majority of users reported they were very satisfied with the information provided (n = 472, 83%). Over half of users (n = 335, 60%) shared or planned to share the information with their health care provider, and 51% (n = 286) reported that the information made an impact on treatment or quality of life. For 96.2% of users (n = 545), some or all of the information provided had not been received through any other source. DISCUSSION: The results demonstrate that, despite the end-user driven Internet, patients and families are not able to find all the information they need on their own. Expert searching remains an important role for librarians working with consumer health information seekers. [Abstract/Link to Full Text]

Delwiche FA, Hall EF
Mapping the literature of athletic training.
J Med Libr Assoc. 2007 Apr;95(2):195-201.
PURPOSE: This paper identifies the core literature of athletic training and determines which major databases provide the most thorough intellectual access to this literature. METHODS: This study collected all cited references from 2002 to 2004 of three journals widely read by those in the athletic training field. Bradford's Law of Scattering was applied to the resulting list to determine the core journal titles in the discipline. Three major databases were reviewed for extent of their coverage of these core journals. RESULTS: Of the total 8,678 citations, one-third referenced a compact group of 6 journals; another third of the citations referenced an additional 40 titles. The remaining 2,837 citations were scattered across 1,034 additional journal titles. CONCLUSIONS: The number and scatter of citations over a three-year period identified forty-six key journals in athletic training. The study results can inform athletic trainers of the core literature in their field, encourage database producers (e.g., MEDLINE, SPORTDiscus, CINAHL) to increase coverage of titles that are not indexed or underindexed, and guide purchasing decisions for libraries serving athletic training programs. [Abstract/Link to Full Text]

Lacroix EM, Collins ME
Interlibrary loan in US and Canadian health sciences libraries 2005: update on journal article use.
J Med Libr Assoc. 2007 Apr;95(2):189-94.
PURPOSE: The authors analyzed 2.48 million interlibrary loan (ILL) requests entered in the National Library of Medicine's (NLM's) DOCLINE system from 3,234 US and Canadian medical libraries during fiscal year (FY) 2005 to study their distribution and nature and the journals in which requested articles were published. METHODS: Data from DOCLINE and NLM's indexing system and online catalog were used to analyze all DOCLINE ILL transactions acted on from October 2004 to September 2005. The authors compared results from this analysis to previous data collected in FY 1992. RESULTS: Overall ILL volume in the United States and Canada is at about the same level as FY 1992 despite marked growth in online searching, knowledge discovery tools, and journals available online. Over 21,000 unique journal titles and 1.4 million unique articles were used to fill 2.2 million ILL requests in FY 2005. Over 1 million of the articles were requested only once by any network library. Fifty-two percent (11,022) of journals had 5 or fewer requests for articles from all the years of a journal by all libraries in the network. Fifty-two percent of the articles requested were published within the most recent 5 years. CONCLUSION: The overall ILL profile in the libraries studied has changed little since FY 1992, notable given other changes in publishing. Small changes, however, may reveal developing trends. Total ILL traffic has been declining in recent years following a peak in 2002, and fewer of the articles requested were published in the most recent five years compared to requests from 1992. [Abstract/Link to Full Text]

Nail-Chiwetalu B, Bernstein Ratner N
An assessment of the information-seeking abilities and needs of practicing speech-language pathologists.
J Med Libr Assoc. 2007 Apr;95(2):182-8, e56-7.
OBJECTIVES: This study assessed the information-seeking practices and needs of speech-language pathologists (SLPs). Improved understanding of these needs can inform librarians and educators to better prepare students in principles and methods of evidence-based practice (EBP) and, through continuing education (CE), promote the integration of EBP into clinical practice of SLPs. METHODS: A 16-question survey was mailed to 1,000 certified speech-language pathologists in the United States. RESULTS: Two hundred and eight usable surveys were returned for a response rate of 21%. For clinical questions, SLPs most often consulted with a colleague, participated in CE activities, and searched the open Internet. Few respondents relied on scholarly journal articles for assistance with clinical cases. The most prominent barriers to finding appropriate information were time and knowledge of where and how to find relevant information. Few reported having information literacy instruction by a librarian. DISCUSSION: If EBP is to become a viable practice in clinical decision making, there appears to be a tremendous need for information literacy instruction in the university curriculum, as well as through CE activities for currently practicing SLPs. Given respondents' reported lack of time and limited access to full-text journals containing evidence relevant to clinical practice, the field of speech-language pathology will need to generate readily accessible clinical summaries of research evidence through meta-analyses, systematic reviews, and clinical practice guidelines. [Abstract/Link to Full Text]

Perley CM, Gentry CA, Fleming AS, Sen KM
Conducting a user-centered information needs assessment: the Via Christi Libraries' experience.
J Med Libr Assoc. 2007 Apr;95(2):173-81, e54-5.
PURPOSE: The research sought to provide evidence to support the development of a long-term strategy for the Via Christi Regional Medical Center Libraries. METHODS: An information needs assessment was conducted in a large medical center serving approximately 5,900 physicians, clinicians, and nonclinical staff in 4 sites in 1 Midwestern city. Quantitative and qualitative data from 1,295 self-reporting surveys, 75 telephone interviews, and 2 focus groups were collected and analyzed to address 2 questions: how could the libraries best serve their patrons, given realistic limitations on time, resources, and personnel, and how could the libraries best help their institution improve patient care and outcomes? RESULTS: Clinicians emphasized the need for "just in time" information accessible at the point of care. Library nonusers emphasized the need to market library services and resources. Both clinical and nonclinical respondents emphasized the need for information services customized to their professional information needs, preferences, and patterns of use. Specific information needs in the organization were identified. DISCUSSION/CONCLUSIONS: The results of this three-part, user-centered information needs assessment were used to develop an evidence-based strategic plan. The findings confirmed the importance of promoting library services in the organization and suggested expanded, collaborative roles for hospital librarians. [Abstract/Link to Full Text]

Ankem K
Information-seeking behavior of women in their path to an innovative alternate treatment for symptomatic uterine fibroids.
J Med Libr Assoc. 2007 Apr;95(2):164-72, e51-3.
OBJECTIVES: The purpose of the study was to discover how women found out about uterine fibroid embolization (UFE) for the treatment of symptomatic uterine fibroids. METHODS: The study retrospectively tracked women from the beginning of their illnesses and analyzed their information-seeking behaviors. Twenty-eight women who had the procedure at the Detroit Medical Center were interviewed using a standard script. Median values and frequencies were calculated to represent information needs, information sources, and perceived helpfulness. Spearman correlations were calculated to find relationships between demographics and information needs. RESULTS: Although the women expressed a great need for almost all types of information (median = 5), those with higher levels of education indicated a greater need to know the reasons that their doctors had for suggesting treatments (r = 0.55). The gathered frequencies indicated that friends, magazines, television, and the Internet were important information sources. A preliminary model of information seeking showed that while friends, magazines, and television made several of the women aware of the new procedure, the Internet was heavily utilized for learning about treatment options. CONCLUSIONS: Health sciences librarians may inform women about their health and treatment options by guiding women to easily readable, authoritative, and reliable information sources, including Web information sites. [Abstract/Link to Full Text]

Meats E, Brassey J, Heneghan C, Glasziou P
Using the Turning Research Into Practice (TRIP) database: how do clinicians really search?
J Med Libr Assoc. 2007 Apr;95(2):156-63.
OBJECTIVES: Clinicians and patients are increasingly accessing information through Internet searches. This study aimed to examine clinicians' current search behavior when using the Turning Research Into Practice (TRIP) database to examine search engine use and the ways it might be improved. METHODS: A Web log analysis was undertaken of the TRIP database-a meta-search engine covering 150 health resources including MEDLINE, The Cochrane Library, and a variety of guidelines. The connectors for terms used in searches were studied, and observations were made of 9 users' search behavior when working with the TRIP database. RESULTS: Of 620,735 searches, most used a single term, and 12% (n = 75,947) used a Boolean operator: 11% (n = 69,006) used "AND" and 0.8% (n = 4,941) used "OR." Of the elements of a well-structured clinical question (population, intervention, comparator, and outcome), the population was most commonly used, while fewer searches included the intervention. Comparator and outcome were rarely used. Participants in the observational study were interested in learning how to formulate better searches. CONCLUSIONS: Web log analysis showed most searches used a single term and no Boolean operators. Observational study revealed users were interested in conducting efficient searches but did not always know how. Therefore, either better training or better search interfaces are required to assist users and enable more effective searching. [Abstract/Link to Full Text]

Dollar DM, Gallagher J, Glover J, Marone RK, Crooker C
Realizing what's essential: a case study on integrating electronic journal management into a print-centric technical services department.
J Med Libr Assoc. 2007 Apr;95(2):147-55.
OBJECTIVE: To support migration from print to electronic resources, the Cushing/Whitney Medical Library at Yale University reorganized its Technical Services Department to focus on managing electronic resources. METHODS: The library hired consultants to help plan the changes and to present recommendations for integrating electronic resource management into every position. The library task force decided to focus initial efforts on the periodical collection. To free staff time to devote to electronic journals, most of the print subscriptions were switched to online only and new workflows were developed for e-journals. RESULTS: Staff learned new responsibilities such as activating e-journals, maintaining accurate holdings information in the online public access catalog and e-journals database ("electronic shelf reading"), updating the link resolver knowledgebase, and troubleshooting. All of the serials team members now spend significant amounts of time managing e-journals. CONCLUSIONS: The serials staff now spends its time managing the materials most important to the library's clientele (e-journals and databases). The team's proactive approach to maintenance work and rapid response to reported problems should improve patrons' experiences using e-journals. The library is taking advantage of new technologies such as an electronic resource management system, and library workflows and procedures will continue to evolve as technology changes. [Abstract/Link to Full Text]

McKibbon KA, Fridsma DB, Crowley RS
How primary care physicians' attitudes toward risk and uncertainty affect their use of electronic information resources.
J Med Libr Assoc. 2007 Apr;95(2):138-46, e49-50.
OBJECTIVE: The research sought to determine if primary care physicians' attitudes toward risk taking or uncertainty affected how they sought information and used electronic information resources when answering simulated clinical questions. METHODS: Using physician-supplied data collected from existing risk and uncertainty scales, twenty-five physicians were classified as risk seekers (e.g., enjoying adventure), risk neutral, or risk avoiders (e.g., cautious) and stressed or unstressed by uncertainty. The physicians then answered twenty-three multiple-choice, clinically focused questions and selected two to pursue further using their own information resources. Think-aloud protocols were used to collect searching process and outcome data (e.g., searching time, correctness of answers, searching techniques). RESULTS: No differences in searching outcomes were observed between the groups. Physicians who were risk avoiding and those who reported stress when faced with uncertainty each showed differences in searching processes (e.g., actively analyzing retrieval, using searching heuristics or rules). Physicians who were risk avoiding tended to use resources that provided answers and summaries, such as Cochrane or UpToDate, less than risk-seekers did. Physicians who reported stress when faced with uncertainty showed a trend toward less frequent use of MEDLINE, when compared with physicians who were not stressed by uncertainty. CONCLUSIONS: Physicians' attitudes towards risk taking and uncertainty were associated with different searching processes but not outcomes. Awareness of differences in physician attitudes may be key in successful design and implementation of clinical information resources. [Abstract/Link to Full Text]

Logan RA
Clinical, classroom, or personal education: attitudes about health literacy.
J Med Libr Assoc. 2007 Apr;95(2):127-37, e48.
PURPOSE: This study explores how diverse attitudes about health literacy are assessed by medical librarians and other health care professionals. PROCEDURES: An online survey of thirty-six items was conducted using Q methodology in two phases in spring 2005 and winter 2006. Respondents (n = 51) were nonrandomly self-selected from a convenience sample of members of the Medical Library Association and a group of environmental health consultants to the National Library of Medicine. FINDINGS: Three factors were identified. Factor 1 is optimistic and supportive of health literacy's transformative sociocultural and professional potential, if clinical settings become a launching point for health literacy activities. Factor 2 is less optimistic about health literacy's potential to improve clinical or patient outcomes and prefers to focus health literacy initiatives on classroom education settings. Factor 3 supports improving the nation's health literacy but tends to support health literacy initiatives when people privately interact with health information materials. CONCLUSIONS: Each factor's attitudes about the appropriate educational venue to initiate health literacy activities are different and somewhat mutually exclusive. This suggests that health literacy is seen through different perceptual frameworks that represent a possible source of professional disagreement. [Abstract/Link to Full Text]

Beauregard JM, Lyon JA, Slovis C
Using the literature to evaluate diagnostic tests: amylase or lipase for diagnosing acute pancreatitis?
J Med Libr Assoc. 2007 Apr;95(2):121-6. [Abstract/Link to Full Text]

Panella NM
Response to Perryman.
J Med Libr Assoc. 2007 Apr;95(2):120. [Abstract/Link to Full Text]

Perryman C
Medicus Deus: a review of factors affecting hospital library services to patients between 1790-1950.
J Med Libr Assoc. 2006 Jul;94(3):263-70.
QUESTION: What are some of the historical societal, medical, and public health trends leading to today's provision of hospital library services to patients? DATA SOURCES: Literature from the archives of the Bulletin of the Medical Library Association and other library sources, medical journals, primary historical documents, and texts from the history of medicine form the core of this review. STUDY SELECTION: The period of review extends from about 1790 through 1950 and focuses solely on trends in the United States. Of primary concern are explicitly documented examples that appear to illustrate the patient-physician relationship and those between librarians and their patient-patrons during the earliest years of the profession's development. DATA EXTRACTION: An historical timeline was created to allow the identification of major trends that may have affected library services. Multiple literature searches were conducted using library, medical, and health anthropology resources. When possible, primary sources were preferred over reviews. MAIN RESULTS: Juxtapositioning historical events allows the reader to obtain an overview of the roots of consumer health services in medical libraries and to consider their potential legacy in today's health care libraries. CONCLUSION: This review article highlights early developments in hospital library service to patients. Further research is needed to verify a preliminary conclusion that in some medical library settings, services to the general public are shaped by the broader health care environment as it has evolved. [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]

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]

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

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

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

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

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

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