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Recent Articles in Journal of Medical Internet Research

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

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

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

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

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

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

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

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

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

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

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

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

Nguyen KD, Hara B, Chlebowski RT
Utility of two cancer organization websites for a multiethnic, public hospital oncology population: comparative cross-sectional survey.
J Med Internet Res. 2005 Jul 1;7(3):e28.
BACKGROUND: While information websites have been developed by major cancer organizations, their appropriateness for patients in multiethnic, multilingual public hospital settings has received limited attention. OBJECTIVE: The objective of the study was to determine the utility of cancer information websites for a public hospital patient population. METHODS: A 70-item questionnaire was developed to evaluate cancer information seeking behavior, Internet access and use, and content appropriateness of two cancer information websites: People Living with Cancer from the American Society of Clinical Oncology (ASCO) and Breast Cancer Info from the Susan Komen Breast Cancer Foundation (SKF). Interviews were conducted with consecutive consenting oncology patients seen in a public hospital oncology clinic. RESULTS: Fifty-nine persons participated in the survey. The response rate was 80%. Participants were Caucasian (25%), African American (19%), Hispanic (42%), and Asian/Pacific Islander (11%). English was the primary language in 53% of participants, 56% had a high school education or less, and 74% had an annual income less than US 35000 dollars. With respect to computer and Internet use, 71% had computer access, and 44% searched for cancer information online, with more being interested in obtaining online information in the future (63%). Participants who had computer access were likely to be English speaking (P = .04). Those less likely to have previously used a computer tended to have a lower annual income (P = .02) or to be males aged 55 years or older (P < .05). When shown sample content from the two websites, almost all participants stated that it was "easy to understand" (ASCO 96%, SKF 96%) and had "easy to understand terms" (ASCO 94%, SKF 92%). Somewhat fewer respondents agreed that the websites provided "information they could use" (ASCO 88%, SKF 80%) or that they would return to these websites (ASCO 73%, SKF 68%). The majority planned to "discuss website information with their oncologists" (ASCO 82%, SKF 70%). CONCLUSIONS: Multiethnic, multilingual cancer patients at a public county hospital commonly had Internet access and found the content of two websites representative of major cancer organizations to be both understandable and useful. [Abstract/Link to Full Text]

Evers KE, Cummins CO, Prochaska JO, Prochaska JM
Online health behavior and disease management programs: are we ready for them? Are they ready for us?
J Med Internet Res. 2005 Jul 1;7(3):e27.
Advancing the science and practice of health promotion and disease management on the Internet requires a systematic program of research examining the population impact of such programs. With impact described as the combination of effectiveness and participation, such research needs to include the examination of the quality and effectiveness of programs that are available to the general public, as well as descriptive and predictive knowledge about population readiness to participate in such programs. There have been few studies examining the quality of interactive health behavior change (HBC) programs on the Internet, and even fewer investigations of the effectiveness of such programs. Based on the review of over 300 HBC programs on the Internet using the "5 A's" of Health Behavior Change on the Internet (HBC-I Screener), which represent standard minimum guidelines for evaluation, it appears HBC on the Internet is in the early stages of development. As health behavior change on the Internet matures from the provision of health information to meeting the requirements necessary to produce health behavior change, and as program developers take advantage of the interactive nature of the Internet, the basic screening and expanded evaluation criteria developed in this project will provide templates for both consumers and developers of programs. The second component necessary for evaluating the impact of HBC on the Internet is the extent to which the population is ready to participate in such programs. We need to move beyond a narrow focus on early adopters and produce a population perspective that includes those not ready, those getting ready, and those ready to use such programs, as well as those already participating. By understanding participation levels of such programs, and what drives this participation, the development and dissemination of practical tailored and targeted interventions can help maximize population participation in Internet programs for health behavior change. [Abstract/Link to Full Text]

Graham AL, Abrams DB
Reducing the cancer burden of lifestyle factors: opportunities and challenges of the Internet.
J Med Internet Res. 2005 Jul 1;7(3):e26.
This paper focuses on the Internet as a tool for enhancing behavior and lifestyle changes to reduce the burden of cancer at a population level. The premise of this paper is that the Internet can and should be leveraged to bridge the chasm between basic science, clinical trials, and public health. Our focus is specifically on the opportunity to disseminate effective behavioral science interventions via the Internet in order to decrease the prevalence of behavioral risk factors for cancer. The examples herein are primarily drawn from tobacco use to illustrate issues that can be applied more generally to other behavioral risk factors for cancer. Four areas will be addressed: (1) the scientific basis and rationale for delivering lifestyle behavior change interventions via the Internet; (2) the need to determine the quality of Internet interventions; (3) methodological considerations in conducting evaluations of Internet interventions; and (4) recommendations for a transdisciplinary approach to Internet intervention development and evaluation. [Abstract/Link to Full Text]

Grama LM, Beckwith M, Bittinger W, Blais D, Lollar C, Middleswarth A, Noone M, Price D, Quint-Kasner S, Shields V, Wright LW
The role of user input in shaping online information from the National Cancer Institute.
J Med Internet Res. 2005 Jul 1;7(3):e25.
The National Cancer Institute (NCI) was among the first federal agencies to recognize the potential of the Internet for disseminating health-related information. The evolution and refinement of NCI's online cancer information has been substantially "user driven"-from the launch of CancerNet in 1995 to the recent redesign of its award-winning successor, the NCI website. This article presents an overview of NCI's multi-pronged approach to gathering input about its online information products, including stakeholder meetings, focus groups, standard and customized online user surveys, usability testing, heuristic reviews, and search log analysis. Also highlighted are some of the many enhancements that have been made to NCI's online cancer information products based on user input. [Abstract/Link to Full Text]

Metz JM, Coyle C, Hudson C, Hampshire M
An Internet-based cancer clinical trials matching resource.
J Med Internet Res. 2005 Jul 1;7(3):e24.
BACKGROUND: Many patients are now accessing the Internet to obtain cancer clinical trials information. However, services offering clinical trials recruitment information have not been well defined. OBJECTIVES: This study describes one of the first Web-based cancer clinical trials matching resources and the demographics of users who were successfully matched. METHODS: OncoLink is the Internet-based educational resource managed by the University of Pennsylvania Cancer Center (UPCC) and serves between 1 and 2 million pages per month to over 385000 unique IP addresses. OncoLink launched one of the first clinical trials matching resources on the Internet that allowed patients to enter demographic data through a secure connection and be matched to clinical trials. For patients with matches to potential trials, appointments were facilitated with the principal investigators. RESULTS: While we did not keep track of patients who could not be matched, 627 patients who submitted online applications between January 2002 and April 2003 were successfully matched for potential enrollment in clinical trials. The mean age of the patient population was 56 years (range 18-88 years). Males represented 60% of the patient population, and over 90% of users were Caucasian. Most of the applications were from patients with colorectal cancer (13%), lung cancer (14%), melanoma (10%), and non-Hodgkin's lymphoma (9%). CONCLUSIONS: This report shows that a significant number of patients are willing to use the Internet for enrolling in clinical trials. Care must be taken to reach patients from a variety of socioeconomic and racial backgrounds. This Internet resource helps to facilitate a consultation with a cancer patient who is prescreened and motivated to enroll in clinical trials. [Abstract/Link to Full Text]

Patrick K, Intille SS, Zabinski MF
An ecological framework for cancer communication: implications for research.
J Med Internet Res. 2005 Jul 1;7(3):e23.
The field of cancer communication has undergone a major revolution as a result of the Internet. As recently as the early 1990s, face-to-face, print, and the telephone were the dominant methods of communication between health professionals and individuals in support of the prevention and treatment of cancer. Computer-supported interactive media existed, but this usually required sophisticated computer and video platforms that limited availability. The introduction of point-and-click interfaces for the Internet dramatically improved the ability of non-expert computer users to obtain and publish information electronically on the Web. Demand for Web access has driven computer sales for the home setting and improved the availability, capability, and affordability of desktop computers. New advances in information and computing technologies will lead to similarly dramatic changes in the affordability and accessibility of computers. Computers will move from the desktop into the environment and onto the body. Computers are becoming smaller, faster, more sophisticated, more responsive, less expensive, and--essentially--ubiquitous. Computers are evolving into much more than desktop communication devices. New computers include sensing, monitoring, geospatial tracking, just-in-time knowledge presentation, and a host of other information processes. The challenge for cancer communication researchers is to acknowledge the expanded capability of the Web and to move beyond the approaches to health promotion, behavior change, and communication that emerged during an era when language- and image-based interpersonal and mass communication strategies predominated. Ecological theory has been advanced since the early 1900s to explain the highly complex relationships among individuals, society, organizations, the built and natural environments, and personal and population health and well-being. This paper provides background on ecological theory, advances an Ecological Model of Internet-Based Cancer Communication intended to broaden the vision of potential uses of the Internet for cancer communication, and provides some examples of how such a model might inform future research and development in cancer communication. [Abstract/Link to Full Text]

LaCoursiere SP, Knobf MT, McCorkle R
Cancer patients' self-reported attitudes about the Internet.
J Med Internet Res. 2005 Jul 1;7(3):e22.
BACKGROUND: Increasing numbers of cancer patients are using the Internet, but little is known about their attitudes toward online health care. OBJECTIVE: The purpose of this substudy was to analyze cancer patients' attitudes toward online health care. METHODS: This was a substudy of 41 persons with cancer who used the Internet for health care information and support and who completed the Attitudes Toward Online Health Care (ATOHC) survey. RESULTS: The majority of study participants were married, held graduate degrees, and had high incomes. Using a five-point Likert scale, means for the five dimensions of the ATOHC survey were as follows: community and news 3.22 (SD = 1.01), outcomes 3.20 (SD = 1.08), trusted information and advice 2.73 (SD = 0.66), self-efficacy in evaluating information and intention 3.46 (SD = 0.65), and disclosure 3.15 (SD = 1.06). The average response fell between "About half the time" and "Usually." Favorite websites for content were Medscape and WebMD, while favorite sites for support were WebMD and Mediconsult. CONCLUSIONS: Respondents were generally eager to obtain and offer cancer information and support online, but they were skeptical of unknown sources. They were comfortable both giving and receiving information and support. Respondents were interested in the experiences of other patients and benefited by their direct and indirect interactions with them. Respondents felt that they coped better with their illness and experienced less uncertainty and anxiety as a result of their online experiences. They reported a certain level of trust, primarily for established reputable sources of information, and they were confident in their ability to evaluate the information, including research reports. In addition, cancer patients displayed a healthy skepticism when presented with the option of divulging their personal health information; however, they were willing to provide personal details if, as a result, a website provided them with individualized information. [Abstract/Link to Full Text]

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

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

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

Himmel W, Meyer J, Kochen MM, Michelmann HW
Information needs and visitors' experience of an Internet expert forum on infertility.
J Med Internet Res. 2005;7(2):e20.
BACKGROUND: Patients increasingly use health portals and Web-based expert forums (ask-the-doctor services), but little is known about the specific needs of Internet users visiting such websites, the nature of their requests, or how satisfied they are with Internet health experts. OBJECTIVE: The aim of this study was to analyze the information requests of (mostly female) patients visiting an Internet expert forum on involuntary childlessness and their satisfaction with the experts' feedback. METHODS: We posted an electronic questionnaire on a website hosting an expert forum on involuntary childlessness. The questionnaire was "activated" whenever a visitor sent a question or request to the expert forum. The survey focused on the reasons for visiting the expert forum and whether the visitors were satisfied with the experts' answers to previously posted questions. The free-text questions of visitors who answered the survey were analyzed using Atlas-ti, a software program for qualitative data analysis. RESULTS: Over a period of 6 months, 513 out of 610 visitors (84%) answered the questionnaire. The majority of respondents (65.5%) expected general information about involuntary childlessness, conception, or an evaluation of drugs. Others were concerned about their actual treatment (40.6%) and therapeutic options (28.8%). Out of 225 respondents who had previously contacted the forum, 223 has received an answer, and 123 (55.2%) were satisfied with the experts' answers. About half (105/223) of those users who had previously received an answer from the expert forum stated that they had discussed it with their own doctor. More of these users were satisfied with their subsequent care in fertility clinics than users who did not talk to their doctor about their Internet activities (93.9% vs 76.1%; P = .015). According to the qualitative analysis, many requests (n = 194) were more or less trivial, especially those for information on basic aspects of reproduction. More than one-third of visitors (n = 199) sent detailed results of diagnostic tests and asked for a first or second opinion. Requests to the expert forum were also sent in order to obtain emotional support (17%) or to complain about a doctor (15%). CONCLUSIONS: Visitors who sent their laboratory findings to receive a thorough evaluation or a second opinion had a good command of the opportunities that an expert forum offers. One important expectation of the forum was emotional support, indicating psychological needs that were not met by medical providers. Future websites must find a compromise in order to protect experts from being overwhelmed by general, nonspecific requests while supporting patients with individualized answers. [Abstract/Link to Full Text]

Campbell RJ, Nolfi DA
Teaching elderly adults to use the Internet to access health care information: before-after study.
J Med Internet Res. 2005;7(2):e19.
BACKGROUND: Much has been written about the Internet's potential to revolutionize health care delivery. As younger populations increasingly utilize Internet-based health care information, it will be essential to ensure that the elderly become adept at using this medium for health care purposes, especially those from minority, low income, and limited educational backgrounds. OBJECTIVE: This paper presents the results of a program designed to teach elderly adults to use the Internet to access health care information. The objective was to examine whether the training led to changes in participant's perceptions of their health, perceptions of their interactions with health care providers, health information-seeking behaviors, and self-care activities. METHODS: Participants attended a 5-week training course held in public libraries and senior community centers within the greater Pittsburgh and Allegheny County region. Classes within each seminar lasted 2 hours and consisted of lecture and hands-on training. Baseline surveys were administered prior to the course, 5-week follow-up surveys were administered immediately after the course, and final surveys were mailed 1 year later. Instruments included the Multidimensional Health Locus of Control (MHLC) Scale, which measures three domains of locus of control (internal, external, and chance); the Krantz Health Opinion Survey (HOS); and the Lau, Hartman, and Ware Health Value Survey. Two additional questionnaires included multiple choice and qualitative questions designed to measure participants' Internet utilization and levels of health care participation. The Health Participation Survey was administered with the baseline survey. The Internet Use Survey was administered at the 1-year mark and contained several items from the Health Participation Survey, which allowed comparison between baseline and 1-year responses. RESULTS: Of the60 elderly adults who began the training course, 42 (mean age 72) completed the entire 5-week training program and the 5-week follow-up questionnaire administered immediately after the program, and 27 completed the 1-year follow-up survey. Statistically significant differences were found between baseline and 5-week follow-up results for MHLC chance subscores in males (P = .02) and females (P = .05), as well as total HOS information seeking scores (P = .05). However, these statistically significant findings disappeared when all 60 original participants were included using a "last observation carried forward" imputation. No statistically significant changes were found between baseline and 5-week follow-up surveys for MHLC external (P = .44) and internal (P = .97) locus of control scores in both genders, or for the HOS behavioral involvement subscale (P = .65). CONCLUSIONS: We failed to show robust before-after effects for most of the outcomes measured. Elderly adults may be willing to use the Internet as a source for general health information; however, when making decisions about their health care, our participants seemed to adhere to a physician-centered model of care. Demographic and situational variables may play a large role in determining which seniors will use the Internet for making behavioral decisions about their health care and in which scenarios they will do so. [Abstract/Link to Full Text]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Recent Articles in BMC Bioinformatics

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Wang AX, Ruzzo WL, Tompa M
How accurately is ncRNA aligned within whole-genome multiple alignments?
BMC Bioinformatics. 2007 Oct 26;8(1):417.
ABSTRACT: BACKGROUND: Multiple alignment of DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated. RESULTS: We evaluate the alignment accuracy of certain noncoding regions using ncRNA alignments from Rfam as a reference. We inspect the MULTIZ alignments from the UCSC Genome Browser for all the human sequences in the Rfam seed alignments. In particular, we find 638 instances of chimeric and partial alignments to human noncoding RNA elements, of which at least 225 can be improved by straightforward means. As a byproduct of our procedure, we predict many novel ncRNA elements that are suggested by the alignment. CONCLUSIONS: MULTIZ does a fairly accurate job of aligning 17 vertebrate genomes in these regions. However, our experiments indicate that better alignments exist in some regions. [Abstract/Link to Full Text]

Barthel D, Hirst JD, Blazewicz J, Burke EK, Krasnogor N
ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information.
BMC Bioinformatics. 2007 Oct 26;8(1):416.
ABSTRACT: BACKGROUND: We introduce the decision support system for "Protein (Structure) Comparison, Knowledge, Similarity and Information" (ProCKSI). ProCKSI integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. It employs the "Universal Similarity Metric" (USM), the "Maximum Contact Map Overlap" (MaxCMO) of protein structures and other external methods such as the "DaliLite" and the "TM-align" methods, the "Combinatorial Extension" (CE) of the optimal path, and the "FAST Align and Search Tool" (FAST). Additionally, ProCKSI allows the user to upload a user-defined similarity matrix supplementing the methods mentioned, and computes a similarity consensus in order to provide a rich, integrated, multicriteria view of large datasets of protein structures. RESULTS: We present ProCKSI's architecture and workflow describing its intuitive user interface, and show its potential on three distinct test-cases. In the first case, ProCKSI is used to evaluate the results of a previous CASP competition, assessing the similarity of proposed models for given targets where the structures could have a large deviation from one another. To perform this type of comparison reliably, we introduce a new consensus method. The second study deals with the verification of a classification scheme for protein kinases, originally derived by "sequence" comparison by Hanks and Hunter, but here we use a consensus similarity measure based on "structures". In the third experiment using the Rost and Sander dataset (RS126), we investigate how a combination of different sets of similarity measures influences the quality and performance of ProCKSI's new consensus measure. ProCKSI performs well with all three datasets, showing its potential for complex, simultaneous multi-method assessment of structural similarity in large protein datasets. Furthermore, combining different similarity measures is usually more robust than relying on one single, unique measure. CONCLUSIONS: Based on a diverse set of similarity measures, ProCKSI computes a consensus similarity profile for the entire protein set. All results can be clustered, visualised, analysed and easily compared with each other through a simple and intuitive interface. ProCKSI is publicly available at "http://www.procksi.net" for academic and non-commercial use. [Abstract/Link to Full Text]

Gormley M, Dampier W, Ertel A, Karacali B, Tozeren A
Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets.
BMC Bioinformatics. 2007 Oct 26;8(1):415.
ABSTRACT: BACKGROUND: Independently derived expression profiles of the same biological condition often have few genes in common. In this study, we created populations of expression profiles from publicly available microarray datasets of cancer (breast, lymphoma and renal) samples linked to clinical information with an iterative machine learning algorithm. ROC curves were used to assess the prediction error of each profile for classification. We compared the prediction error of profiles correlated with molecular phenotype against profiles correlated with relapse-free status. Prediction error of profiles identified with supervised univariate feature selection algorithms were compared to profiles selected randomly from a) all genes on the microarray platform and b) a list of known disease-related genes (a priori selection). We also determined the relevance of expression profiles on test arrays from independent datasets, measured on either the same or different microarray platforms. RESULTS: Highly discriminative expression profiles were produced on both simulated gene expression data and expression data from breast cancer and lymphoma datasets on the basis of ER and BCL-6 expression, respectively. Use of relapse-free status to identify profiles for prognosis prediction resulted in poorly discriminative decision rules. Supervised feature selection resulted in more accurate classifications than random or a priori selection, however, the difference in prediction error decreased as the number of features increased. These results held when decision rules were applied across-datasets to samples profiled on the same microarray platform. CONCLUSIONS: Our results show that many gene sets predict molecular phenotypes accurately. Given this, expression profiles identified using different training datasets should be expected to show little agreement. In addition, we demonstrate the difficulty in predicting relapse directly from microarray data using supervised machine learning approaches. These findings are relevant to the use of molecular profiling for the identification of candidate biomarker panels. [Abstract/Link to Full Text]

Sun J, Sun Y, Ding G, Liu Q, Wang C, He Y, Shi T, Li Y, Zhao Z
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes.
BMC Bioinformatics. 2007 Oct 26;8(1):414.
ABSTRACT: BACKGROUND: Although many genomic features have been used in the prediction of protein-protein interactions (PPIs), frequently only one is used in a computational method. After realizing the limited power in the prediction using only one genomic feature, investigators are now moving toward integration. So far, there have been few integration studies for PPI prediction; one failed to yield appreciable improvement of prediction and the others did not conduct performance comparison. It remains unclear whether an integration of multiple genomic features can improve the PPI prediction and, if it can, how to integrate these features. RESULTS: In this study, we first performed a systematic evaluation on the PPI prediction in Escherichia coli (E. coli) by four genomic context based methods: the phylogenetic profile method, the gene cluster method, the gene fusion method, and the gene neighbor method. The number of predicted PPIs and the average degree in the predicted PPI networks varied greatly among the four methods. Further, no method outperformed the others when we tested using three well-defined positive datasets from the KEGG, EcoCyc, and DIP databases. Based on these comparisons, we developed a novel integrated method, named InPrePPI. InPrePPI first normalizes the AC value (an integrated value of the accuracy and coverage) of each method using three positive datasets, then calculates a weight for each method, and finally uses the weight to calculate an integrated score for each protein pair predicted by the four genomic context based methods. We demonstrate that InPrePPI outperforms each of the four individual methods and, in general, the other two existing integrated methods: the joint observation method and the integrated prediction method in STRING. These four methods and InPrePPI are implemented in a user-friendly web interface. CONCLUSION: This study evaluated the PPI prediction by four genomic context based methods, and presents an integrated evaluation method that shows better performance in E. coli. [Abstract/Link to Full Text]

Irons DJ, Monk NA
Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network.
BMC Bioinformatics. 2007 Oct 25;8(1):413.
ABSTRACT: BACKGROUND: It is widely accepted that genetic regulatory systems are 'modular', in that the whole system is made up of smaller 'subsystems' corresponding to specific biological functions. Most attempts to identify modules in genetic regulatory systems have relied on the topology of the underlying network. However, it is the temporal activity (dynamics) of genes and proteins that corresponds to biological functions, and hence it is dynamics that we focus on here for identifying subsystems. RESULTS: Using Boolean network models as an exemplar, we present a new technique to identify subsystems, based on their dynamical properties. The main part of the method depends only on the stable dynamics (attractors) of the system, thus requiring no prior knowledge of the underlying network. However, knowledge of the logical relationships between the network components can be used to describe how each subsystem is regulated. To demonstrate its applicability to genetic regulatory systems, we apply the method to a model of the Drosophila segment polarity network, providing a detailed breakdown of the system. CONCLUSIONS: We have designed a technique for decomposing any set of discrete-state, discrete-time attractors into subsystems. Having a suitable mathematical model also allows us to describe how each subsystem is regulated and how robust each subsystem is against perturbations. However, since the subsystems are found directly from the attractors, a mathematical model or underlying network topology is not necessarily required to identify them, potentially allowing the method to be applied directly to experimental expression data. [Abstract/Link to Full Text]

Chen J, Hsueh HM, Delongchamp R, Lin CJ, Tsai CA
Reproducibility of microarray data: a further analysis of microarray quality control (MAQC)data.
BMC Bioinformatics. 2007 Oct 25;8(1):412.
ABSTRACT: BACKGROUND: Many researchers are concerned with the comparability and reliability of microarray gene expression data. Recent completion of the MicroArray Quality Control (MAQC) project provides a unique opportunity to assess reproducibility across multiple sites and the comparability across multiple platforms. The MAQC analysis presented for the conclusion of inter- and intra-platform comparability/reproducibility of microarray gene expression measurements is inadequate. We evaluate the reproducibility/comparability of the MAQC data for 12901 common genes in four titration samples generated from five high-density one-color microarray platforms and the TaqMan technology. We discuss some of the problems with the use of correlation coefficient as metric to evaluate the inter- and intra-platform reproducibility and the percent of overlapping genes (POG) as a measure for evaluation of a gene selection procedure by MAQC. RESULTS: A total of 293 arrays is used in the intra- and inter-platform analysis. A hierarchical cluster analysis shows distinct differences in the measured intensities among the five platforms. A number of genes show a small fold-change in one platform and a large fold-change in another platform, even though the correlations between platforms are high. An analysis of variance shows thirty percent of gene expressions of the samples show inconsistent patterns across the five platforms. We illustrated that POG does not reflect the accuracy of a selected gene list. A non-overlapping gene can be truly differentially expressed with a stringent cut, and an overlapping gene can be non-differentially expressed with non-stringent cutoff. In addition, POG is an unusable selection criterion. POG can increase or decrease irregularly as cutoff changes; there is no criterion to determine a cutoff so that POG is optimized. CONCLUSIONS: Using various statistical methods we demonstrate that there are differences in the intensities measured by different platforms and different sites within platform. Within each platform, the patterns of expression are generally consistent, but there is site-by-site variability. Evaluation of data analysis methods for use in regulatory decision should take no treatment effect into consideration, when there is no treatment effect, "a fold-change cutoff with a non-stringent p-value cutoff" could result in 100% false positive error selection. [Abstract/Link to Full Text]

Gasbarra D, Pirinen M, Sillanpaa MJ, Arjas E
Estimating genealogies from linked marker data: a Bayesian approach.
BMC Bioinformatics. 2007 Oct 25;8(1):411.
ABSTRACT: BACKGROUND: Answers to several fundamental questions in statistical genetics would ideally require knowledge of the ancestral pedigree and of the gene flow therein. A few examples of such questions are haplotype estimation, relatedness and relationship estimation, gene mapping by combining pedigree and linkage disequilibrium information, and estimation of population structure. RESULTS: We present a probabilistic method for genealogy reconstruction. Starting with a group of genotyped individuals from some population isolate, we explore the state space of their possible ancestral histories under our Bayesian model by using Markov chain Monte Carlo (McMC) sampling techniques. The main contribution of our work is the development of sampling algorithms in the resulting vast state space with highly dependent variables. The main drawback is the computational complexity that limits the time horizon within which explicit reconstructions can be carried out in practice. CONCLUSIONS: The estimates for IBD (identity-by-descent) and haplotype distributions are tested in several settings using simulated data. The results appear to be promising for a further development of the method. [Abstract/Link to Full Text]

Islamaj Dogan R, Getoor L, Wilbur WJ, Mount SM
Features generated for computational splice-site prediction correspond to functional elements.
BMC Bioinformatics. 2007 Oct 24;8(1):410.
ABSTRACT: BACKGROUND: Accurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and introns. We previously described a feature generation algorithm (FGA) that is capable of achieving high classification accuracy on human 3' splice sites. In this paper, we extend the splice-site prediction to 5' splice sites and explore the generated features for biologically meaningful splicing signals. RESULTS: We present examples from the observed features that correspond to known signals, both core signals (including the branch site and pyrimidine tract) and auxiliary signals (including GGG triplets and exon splicing enhancers). We present evidence that features identified by FGA include splicing signals not found by other methods. CONCLUSIONS: Our generated features capture known biological signals in the expected sequence interval flanking splice sites. The method can be easily applied to other species and to similar classification problems, such as tissue-specific regulatory elements, polyadenylation sites, promoters, etc. [Abstract/Link to Full Text]

Smith MV, Miller CR, Kohn M, Walker NJ, Portier CJ
Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process.
BMC Bioinformatics. 2007 Oct 23;8(1):409.
ABSTRACT: BACKGROUND: Since real time PCR was first developed, several approaches to estimating the initial quantity of template in an RT-PCR reaction have been tried. While initially only the early thermal cycles corresponding to exponential duplication were used, lately there has been an effort to use all of the cycles in a PCR. The efforts have included both fitting empirical sigmoid curves and more elaborate mechanistic models that explore the chemical reactions taking place during each cycle. The more elaborate mechanistic models require many more parameters than can be fit from a single amplification, while the empirical models provide little insight and are difficult to tailor to specific reactants. RESULTS: We directly estimate the initial amount of amplicon using a simplified mechanistic model based on chemical reactions in the annealing step of the PCR. The basic model includes the duplication of DNA with the digestion of Taqman probe and the re-annealing between previously synthesized DNA strands of opposite orientation. By modelling the amount of Taqman probe digested and matching that with the observed fluorescence, the conversion factor between the number of fluorescing dye molecules and observed fluorescent emission can be estimated, along with the absolute initial amount of amplicon and the rate parameter for re-annealing. The model is applied to several PCR reactions with known amounts of amplicon and is shown to work reasonably well. An expanded version of the model allows duplication of amplicon without release of fluorescent dye, by adding 1 more parameter to the model. The additional process is helpful in most cases where the initial primer concentration exceeds the initial probe concentration. Software for applying the algorithm to data may be downloaded at http://www.niehs.nih.gov/research/resources/software/pcranalyzer/ CONCLUSIONS: We present proof of the principle that a mechanistically based model can be fit to observations from a single PCR amplification. Initial amounts of amplicon are well estimated without using a standard solution. Using the ratio of the predicted initial amounts of amplicon from 2 PCRs is shown to work well even when the absolute amounts of amplicon are underestimated in the individual PCRs. [Abstract/Link to Full Text]

Maraziotis IA, Dimitrakopoulou K, Bezerianos A
Growing functional modules from a seed protein via integration of protein interaction and gene expression data.
BMC Bioinformatics. 2007 Oct 23;8(1):408.
ABSTRACT: BACKGROUND: Nowadays modern biology aims at unravelling the strands of complex biological structures such as the protein-protein interactions (PPI) networks. A key concept in the organization of PPI networks is the existence of dense subnetworks (functional modules) in them. In recent approaches clustering algorithms were applied at these networks and the resulting subnetworks were evaluated by estimating the coverage of well-established protein complexes they contained. However, most of these algorithms elaborate on an unweighted graph structure which in turn fails to elevate those interactions that would contribute to the construction of biologically more valid and coherent functional modules. RESULTS: In the current study, we present a method that corroborates the integration of protein interaction and microarray data via the discovery of biologically meaningful functional modules. Initially the gene expression information is overlaid as weights onto the PPI network and the enriched PPI graph allows us to exploit its topological aspects, while simultaneously highlights enhanced functional association in specific pairs of proteins. Then we present an algorithm that unveils the functional modules of the weighted graph by expanding a kernel protein set, which originates from a given seed protein used as starting-point. CONCLUSIONS: The integrated data and the concept of our approach provide reliable functional modules. We give proofs based on yeast data that our method manages to give accurate results in terms both of structural coherency, as well as functional consistency. [Abstract/Link to Full Text]

Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM
Bioinformatic identification of novel putative photoreceptor specific cis-elements.
BMC Bioinformatics. 2007 Oct 22;8(1):407.
ABSTRACT: BACKGROUND: Cell specific gene expression is largely regulated by different combinations of transcription factors that bind cis-elements in the upstream promoter sequence. However, experimental detection of cis-elements is difficult, expensive, and time-consuming. This provides a motivation for developing bioinformatic methods to identify cis-elements that could prioritize future experimental studies. Here, we use motif discovery algorithms to predict transcription factor binding sites involved in regulating the differences between murine rod and cone photoreceptor populations. RESULTS: To identify highly conserved motifs enriched in promoters that drive expression in either rod or cone photoreceptors, we assembled a set of murine rod-specific, cone-specific, and non-photoreceptor background promoter sequences. These sets were used as input to a newly devised motif discovery algorithm called Iterative Alignment/Modular Motif Selection (IAMMS). Using IAMMS, we predicted 34 motifs that may contribute to rod-specific (19 motifs) or cone-specific (15 motifs) expression patterns. Of these, 16 rod- and 12 cone-specific motifs were found in clusters near the transcription start site. New findings include the observation that cone promoters tend to contain TATA boxes, while rod promoters tend to be TATA-less (exempting Rho and Cnga1). Additionally, we identify putative sites for IL-6 effectors (in rods) and RXR family members (in cones) that can explain experimental data showing changes to cell-fate by activating these signaling pathways during rod/cone development. Two of the predicted motifs (NRE and ROP2) have been confirmed experimentally to be involved in cell-specific expression patterns. We provide a full database of predictions as additional data that may contain further valuable information. IAMMS predictions are compared with existing motif discovery algorithms, DME and BioProspector. We find that over 60% of IAMMS predictions are confirmed by at least one other motif discovery algorithm. CONCLUSIONS: We predict novel, putative cis-elements enriched in the promoter of rod-specific or cone-specific genes. These are candidate binding sites for transcription factors involved in maintaining functional differences between rod and cone photoreceptor populations. [Abstract/Link to Full Text]

Lombardot T, Kottmann R, Giuliani G, de Bono A, Addor N, Glockner FO
MetaLook: a 3D visualisation software for marine ecological genomics.
BMC Bioinformatics. 2007 Oct 22;8(1):406.
ABSTRACT: BACKGROUND: Marine ecological genomics can be defined as the application of genomic sciences to understand the structure and function of marine ecosystems. In this field of research, the analysis of genomes and metagenomes of environmental relevance must take into account the corresponding habitat (contextual) data, e.g. water depth, physical and chemical parameters. The creation of specialised software tools and databases is requisite to allow this new kind of integrated analysis. RESULTS: We implemented the MetaLook software for visualisation and analysis of marine ecological genomic and metagenomic data with respect to habitat parameters. MetaLook offers a three-dimensional user interface to interactively visualise DNA sequences on a world map, based on a centralised georeferenced database. The user can define environmental containers to organise the sequences according to different habitat criteria. To find similar sequences, the containers can be queried with either genes from the georeferenced database or user-imported sequences, using the BLAST algorithm. This allows an interactive assessment of the distribution of gene functions in the environment. CONCLUSIONS: MetaLook allows scientists to investigate sequence data in their environmental context and to explore correlations between genes and habitat parameters. This software is a step towards the creation of specialised tools to study constrained distributions and habitat specificity of genes correlated with specific processes. [Abstract/Link to Full Text]

Stamatakis A, Auch AF, Meier-Kolthoff J, Goeker M
AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa.
BMC Bioinformatics. 2007 Oct 22;8(1):405.
ABSTRACT: BACKGROUND: Current tools for Co-phylogenetic analyses are not able to cope with the continuous accumulation of phylogenetic data. The sophisticated statistical test for host-parasite co-phylogenetic analyses implemented in Parafit does not allow it to handle large datasets in reasonable times. The Parafit and DistPCoA programs are the by far most compute-intensive components of the Parafit analysis pipeline. We present AxParafit and AxPcoords (Ax stands for Accelerated) which are highly optimized versions of Parafit and DistPCoA respectively. RESULTS: Both programs have been entirely re-written in C. Via optimization of the algorithm and the C code as well as integration of highly tuned BLAS and LAPACK methods AxParafit runs 5-61 times faster than Parafit with a lower memory footprint (up to 35% reduction) while the performance benefit increases with growing dataset size. The MPI-based parallel implementation of AxParafit shows good scalability on up to 128 processors, even on medium-sized datasets. The parallel analysis with AxParafit on 128 CPUs for a medium-sized dataset with an 512 by 512 association matrix is more than 1,200/128 times faster per processor than the sequential Parafit run. AxPcoords is 8-26 times faster than DistPCoA and numerically stable on large datasets. We outline the substantial benefits of using parallel AxParafit by example of a large-scale empirical study on smut fungi and their host plants. To the best of our knowledge, this study represents the largest co-phylogenetic analysis to date. CONCLUSIONS: The highly efficient AxPcoords and AxParafit programs allow for large-scale co-phylogenetic analyses on several thousands of taxa for the first time. In addition, AxParafit and AxPcoords have been integrated into the easy-to-use CopyCat tool. [Abstract/Link to Full Text]

Taguchi YH, Gromiha MM
Application of amino acid occurrence for discriminating different folding types of globular protein.
BMC Bioinformatics. 2007 Oct 22;8(1):404.
ABSTRACT: BACKGROUND: Predicting the three-dimensional structure of a protein from its amino acid sequence is a long-standing goal in computational/molecular biology. The discrimination of different structural classes and folding types are intermediate steps in protein structure prediction. RESULTS: In this work, we have proposed a method based on linear discriminant analysis (LDA) for discriminating 30 different folding types of globular proteins using amino acid occurrence. Our method was tested with a non-redundant set of 1612 proteins and it discriminated them with the accuracy of 38\%, which is comparable to or better than other methods in the literature. A web server has been developed for discriminating the folding type of a query protein from its amino acid sequence and it is available at http://granular.com/PROLDA/. CONCLUSIONS: Amino acid occurrence has been successfully used to discriminate different folding types of globular proteins. The discrimination accuracy obtained with amino acid occurrence is better than that obtained with amino acid composition and/or amino acid properties. In addition, the method is very fast to obtain the results. \end{abstract} [Abstract/Link to Full Text]

Dalevi D, Desantis TZ, Fredslund J, Andersen GL, Markowitz VM, Hugenholtz P
Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool.
BMC Bioinformatics. 2007 Oct 18;8(1):402.
ABSTRACT: BACKGROUND: Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence database. Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies. Description: We have developed an automated iterative procedure for delineating stable (monophyletic) hierarchical groups to large (or small) trees and naming those groups according to a set of sequentially applied rules. In addition, we have created an associated ungrouping tool for removing existing groups that do not meet user-defined criteria (such as monophyly). The procedure is implemented in a program called GRUNT (GRouping, Ungrouping, Naming Tool) and has been applied to the current release of the Greengenes (Hugenholtz) 16S rRNA gene taxonomy comprising more than 130,000 taxa. CONCLUSION: GRUNT will facilitate researchers requiring comprehensive hierarchical grouping of large tree topologies in, for example, database curation, microarray design and pangenome assignments. The application is available at greengenes.lbl.gov/GRUNT. [Abstract/Link to Full Text]

Gilchrist MA, Qin H, Zaretzki R
Modeling SAGE tag formation and its effects on data interpretation within a Bayesian framework.
BMC Bioinformatics. 2007 Oct 18;8(1):403.
ABSTRACT: BACKGROUND: Serial Analysis of Gene Expression (SAGE) is a high-throughput method for inferring mRNA expression levels from the experimentally generated sequence based tags. Standard analyses of SAGE data, however, ignore the fact that the probability of generating an observable tag varies across genes and between experiments. As a consequence, these analyses result in biased estimators and posterior probability intervals for gene expression levels in the transcriptome. RESULTS: Using the yeast Saccharomyces cerevisiae as an example, we introduce a new Bayesian method of data analysis which is based on a model of SAGE tag formation. Our approach incorporates the variation in the probability of tag formation into the interpretation of SAGE data and allows us to derive exact joint and and approximate marginal posterior distributions for the mRNA frequency of genes detectable using SAGE. Our analysis of these distributions indicates that the frequency of a gene in the tag pool is influenced by its mRNA frequency, the cleavage efficiency of the anchoring enzyme (AE), and the number of informative and uninformative AE cleavage sites within its mRNA. CONCLUSIONS: With a mechanistic, model based approach for SAGE data analysis, we find that inter-genic variation in SAGE tag formation is large. However, this variation can be estimated and, importantly, accounted for using the methods we develop here. As a result, SAGE based estimates of mRNA frequencies can be adjusted to remove the bias introduced by the SAGE tag formation process. [Abstract/Link to Full Text]

Cote RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H
The Protein Identifier Cross-Reference (PICR) service: reconciling protein identifiers across multiple source databases.
BMC Bioinformatics. 2007 Oct 18;8(1):401.
ABSTRACT: BACKGROUND: Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. RESULTS: We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. CONCLUSIONS: We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at http://www.ebi.ac.uk/Tools/picr. [Abstract/Link to Full Text]

Sclep G, Allemeersch J, Liechti R, De Meyer B, Beynon J, Bhalerao R, Moreau Y, Nietfeld W, Renou JP, Reymond P, Kuiper MT, Hilson P
CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes.
BMC Bioinformatics. 2007 Oct 18;8(1):400.
ABSTRACT: BACKGROUND: The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries [1] to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research community. The CATMA initiative offers the power and flexibility to regularly update the GST collection according to evolving knowledge about the gene repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference. RESULTS: GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts, TIGR5 and PSB-EuGene, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an improved version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA. Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 protein-encoding nuclear gene models in the TAIR6 and EuGene genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition. CONCLUSIONS: To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA repertoire is available through the CATMA database (www.catma.org). [Abstract/Link to Full Text]

Wu RZ, Chaivorapol C, Zheng J, Li H, Liang S
fREDUCE: Detection of degenerate regulatory elements using correlation with expression.
BMC Bioinformatics. 2007 Oct 17;8(1):399.
ABSTRACT: BACKGROUND: The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. A major challenge is to decipher transcription factor binding sites from sequence and functional genomic data using computational means. While current methods can detect strong binding sites, they are less sensitive to degenerate motifs, especially those occurring in only a small number of putative target genes. RESULTS: We present fREDUCE, a computational method specialized for the detection of weak or degenerate binding motifs from gene expression or ChIP-chip data. fREDUCE is built upon the widely applied program REDUCE, which elicits motifs by global statistical correlation of motif counts with expression data. fREDUCE introduces several algorithmic refinements that allow efficient exhaustive searches of oligonucleotides with a specified number of degenerate IUPAC symbols. On yeast ChIP-chip benchmarks, fREDUCE correctly identified motifs and their degeneracies with accuracies greater than its predecessor REDUCE as well as other known motif-finding programs. We have also used fREDUCE to make novel motif predictions for transcription factors with poorly characterized binding sites. CONCLUSIONS: We demonstrate that fREDUCE is a valuable tool for the prediction of degenerate transcription factor binding sites, especially from array datasets with weak signals that may elude other motif detection methods. [Abstract/Link to Full Text]

Eppley JM, Tyson GW, Getz WM, Banfield JF
Strainer: software for analysis of population variation in community genomic datasets.
BMC Bioinformatics. 2007;8398.
BACKGROUND: Metagenomic analyses of microbial communities that are comprehensive enough to provide multiple samples of most loci in the genomes of the dominant organism types will also reveal patterns of genetic variation within natural populations. New bioinformatic tools will enable visualization and comprehensive analysis of this sequence variation and inference of recent evolutionary and ecological processes. RESULTS: We have developed a software package for analysis and visualization of genetic variation in populations and reconstruction of strain variants from otherwise co-assembled sequences. Sequencing reads can be clustered by matching patterns of single nucleotide polymorphisms to generate predicted gene and protein variant sequences, identify conserved intergenic regulatory sequences, and determine the quantity and distribution of recombination events. CONCLUSION: The Strainer software, a first generation metagenomic bioinformatics tool, facilitates comprehension and analysis of heterogeneity intrinsic in natural communities. The program reveals the degree of clustering among closely related sequence variants and provides a rapid means to generate gene and protein sequences for functional, ecological, and evolutionary analyses. [Abstract/Link to Full Text]

Livesay DR, Kidd PD, Eskandari S, Roshan U
Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family.
BMC Bioinformatics. 2007 Oct 17;8(1):397.
ABSTRACT: BACKGROUND: Efforts to predict functional sites from globular proteins is increasingly common; however, the most successful of these methods generally require structural insight. Unfortunately, despite several recent technological advances, structural coverage of membrane integral proteins continues to be sparse. Consequently, sequence-based methods represent an important alternative to illuminate functional roles. In this report, we critically examine the ability of several computational methods to provide functional insight within two specific areas. First, can phylogenomic methods accurately describe the functional diversity across a membrane integral protein family? And second, can sequence-based strategies accurately predict key functional sites? Due to the presence of a recently solved structure and a vast amount of experimental mutagenesis data, the neurotransmitter/Na+ symporter (NSS) family is an ideal model system to assess the quality of our predictions. RESULTS: The raw NSS sequence dataset contains 181 sequences, which have been aligned by various methods. The resultant phylogenetic trees always contain six major subfamilies are consistent with the functional diversity across the family. Moreover, in well-represented subfamilies, phylogenetic clustering recapitulates several nuanced functional distinctions. Functional sites are predicted using six different methods (phylogenetic motifs, two methods that identify subfamily-specific positions, and three different conservation scores). A canonical set of 34 functional sites identified by Yamashita et al. within the recently solved LeuTAa structure is used to assess the quality of the predictions, most of which are predicted by the bioinformatic methods. Remarkably, the importance of these sites is largely confirmed by experimental mutagenesis. Furthermore, the collective set of functional site predictions qualitatively clusters along the proposed transport pathway, further demonstrating their utility. Interestingly, the various prediction schemes provide results that are predominantly orthogonal to each other. However, when the methods do provide overlapping results, specificity is shown to increase dramatically (e.g., sites predicted by any three methods have both accuracy and coverage greater than 50%). CONCLUSIONS: The results presented herein clearly establish the viability of sequence-based bioinformatic strategies to provide functional insight within the NSS family. As such, we expect similar bioinformatic investigations will streamline functional investigations within membrane integral families in the absence of structure. [Abstract/Link to Full Text]

Wittkop T, Baumbach J, Lobo FP, Rahmann S
Large scale clustering of protein sequences with FORCE -- A layout based heuristic for weighted cluster editing.
BMC Bioinformatics. 2007 Oct 17;8(1):396.
ABSTRACT: BACKGROUND: Detecting groups of functionally related proteins from their amino acid sequence alone has been a long-standing challenge in computational genome research. Several clustering approaches, following different strategies, have been published to attack this problem. Today, new sequencing technologies provide huge amounts of sequence data that has to be efficiently clustered with constant or increased accuracy, at increased speed. RESULTS: We advocate that the model of weighted cluster editing, also known as transitive graph projection is well-suited to protein clustering. We present the FORCE heuristic that is based on transitive graph projection and clusters arbitrary sets of objects, given pairwise similarity measures. In particular, we apply FORCE to the problem of protein clustering and show that it outperforms the most popular existing clustering tools (Spectral clustering, TribeMCL, GeneRAGE, Hierarchical clustering, and Affinity Propagation). Furthermore, we show that FORCE is able to handle huge datasets by calculating clusters for all 192,187 prokaryotic protein sequences (66 organisms) obtained from the COG database. Finally, FORCE is integrated into the corynebacterial reference database CoryneRegNet. CONCLUSIONS: FORCE is an applicable alternative to existing clustering algorithms. Its theoretical foundation, weighted cluster editing, can outperform other clustering paradigms on protein homology clustering. FORCE is open source and implemented in Java. The software, including the source code, the clustering results for COG and CoryneRegNet, and all evaluation datasets are available at http://gi.cebitec.uni-bielefeld.de/comet/force/. [Abstract/Link to Full Text]

Ptitsyn AA, Zvonic S, Gimble JM
Permutation test for periodicity in short time series data.
BMC Bioinformatics. 2007;8395. [Abstract/Link to Full Text]

Rueda OM, Diaz-Uriarte R
A response to Yu et al. 'A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array', BMC Bioinformatics 2007, 8: 145.
BMC Bioinformatics. 2007 Oct 16;8(1):394.
ABSTRACT: BACKGROUND: Yu et al.(BMC Bioinformatics 2007,8: 145) have recently compared the performance of several methods for the detection of genomic amplification and deletion breakpoints using data from high-density single nucleotide polymorphism arrays. One of the methods compared is our non-homogenous Hidden Markov Model approach. Our approach uses Markov Chain Monte Carlo for inference, but Yu et al. run the sampler for a severely insufficient number of iterations for a Markov Chain Monte Carlo-based method. Moreover, they did not use the appropriate reference level for the non-altered state. METHODS: We rerun the analysis in Yu et al. using appropriate settings for both the Markov Chain Monte Carlo iterations and the reference level. Additionally, to show how easy it is to obtain answers to additional specific questions, we have added a new analysis targeted specifically to the detection of breakpoints. RESULTS: The reanalysis show that the performance of our method is comparable to that of the other methods analyzed. In addition, we can provide probabilities of a given spot being a breakpoint, something unique among the methods examined. CONCLUSIONS: Markov Chain Monte Carlo methods require using a sufficient number of iterations before they can be assumed to yield samples from the distribution of interest. Running our method with too small a number of iterations cannot be representative of its performance. Moreover, our analysis show how our original approach can be easily adapted to answer specific additional questions (e.g. identify edges). [Abstract/Link to Full Text]

Vinga S, Almeida JS
Local Renyi entropic profiles of DNA sequences.
BMC Bioinformatics. 2007 Oct 16;8(1):393.
ABSTRACT: BACKGROUND: In a recent report the authors presented a new measure of continuous entropy for DNA sequences, which allows the estimation of their randomness level. The definition therein explored was based on the Renyi entropy of probability density estimation (pdf) using the Parzen's window method and applied to Chaos Game Representation/Universal Sequence Maps (CGR/USM). Subsequent work proposed a fractal pdf kernel as a more exact solution for the iterated map representation. This report extends the concepts of continuous entropy by defining DNA sequence entropic profiles using the new pdf estimations to refine the density estimation of motifs. RESULTS: The new methodology enables two results. On the one hand it shows that the entropic profiles are directly related with the statistical significance of motifs, allowing the study of under and over-representation of segments. On the other hand, by spanning the parameters of the kernel function it is possible to extract important information about the scale of each conserved DNA region. The computational applications, developed in Matlab m-code, the corresponding binary executables and additional material and examples are made publicly available at http://kdbio.inesc-id.pt/~svinga/ep/. CONCLUSIONS: The ability to detect local conservation from a scale-independent representation of symbolic sequences is particularly relevant for biological applications where conserved motifs occur in multiple, overlapping scales, with significant future applications in the recognition of foreign genomic material and inference of motif structures. [Abstract/Link to Full Text]

Chen J, Xu H, Aronow BJ, Jegga AG
Improved human disease candidate gene prioritization using mouse phenotype.
BMC Bioinformatics. 2007 Oct 16;8(1):392.
ABSTRACT: BACKGROUND: The majority of common diseases are multi-factorial and modified by genetically and mechanistically complex polygenic interactions and environmental factors. High-throughput genome-wide studies like linkage analysis and gene expression profiling, tend to be most useful for classification and characterization but do not provide sufficient information to identify or prioritize specific disease causal genes. RESULTS: Extending on an earlier hypothesis that the majority of genes that impact or cause disease share membership in any of several functional relationships we, for the first time, show the utility of mouse phenotype data in human disease gene prioritization. We study the effect of different data integration methods, and based on the validation studies, we show that our approach, ToppGene (http://toppgene.cchmc.org), outperforms two of the existing candidate gene prioritization methods, SUSPECTS and ENDEAVOUR. CONCLUSION: The incorporation of phenotype information for mouse orthologs of human genes greatly improves the human disease candidate gene analysis and prioritization. [Abstract/Link to Full Text]

Wang RS, Wang Y, Wu LY, Zhang XS, Chen L
Analysis on multi-domain cooperation for predicting protein-protein interactions.
BMC Bioinformatics. 2007 Oct 16;8(1):391.
ABSTRACT: BACKGROUND: Domains are the basic functional units of proteins. It is believed that protein-protein interactions are realized through domain interactions. Revealing multi-domain cooperation can provide deep insights into the essential mechanism of protein-protein interactions at the domain level and be further exploited to improve the accuracy of protein interaction prediction. RESULTS: In this paper, we aim to identify cooperative domains for protein interactions by extending two-domain interactions to multi-domain interactions. Based on the high-throughput experimental data from multiple organisms with different reliabilities, the interactions of domains were inferred by a Linear Programming algorithm with Multi-domain pairs (LPM) and an Association Probabilistic Method with Multi-domain pairs (APMM). Experimental results demonstrate that our approach not only can find cooperative domains effectively but also has a higher accuracy for predicting protein interaction than the existing methods. Cooperative domains,including strongly cooperative domains and superdomains, were detected from major interaction databases MIPS and DIP, and many of them were verified by physical interactions from the crystal structures of protein complexes in PDB which provide intuitive evidences for such cooperation. Comparison experiments in terms of protein/domain interaction prediction justified the benefit of considering multi-domain cooperation. CONCLUSIONS: From the computational viewpoint, this paper gives a general framework to predict protein interactions in a more accurate manner by considering the information of both multi-domains and multiple organisms, which can also be applied to identify cooperative domains, to reconstruct large complexes and further to annotate functions of domains. Supplementary information and software are provided in http://intelligent.eic.osaka-sandai.ac.jp/chenen/MDCinfer.htm and http://zhangroup.aporc.org/bioinfo/MDCinfer. [Abstract/Link to Full Text]

McLaughlin WA, Chen K, Hou T, Wang W
On the detection of functionally coherent groups of protein domains with an extension to protein annotation.
BMC Bioinformatics. 2007 Oct 16;8(1):390.
ABSTRACT: BACKGROUND: Protein domains coordinate to perform multifaceted cellular functions, and domain combinations serve as the functional building blocks in the cell. Available methods to identify functional domain combinations are be limited in their scope, e.g. to the identification of combinations falling within individual proteins or within specific regions in a translated genome. Further effort is needed to identify groups of domains that span across two or more proteins and are linked by a cooperative function. Such functional domain combinations can be useful for protein annotation. RESULTS: Using a new computational method, we have identified 114 groups of domains, referred to as domain assembly units (DASSEM units), in the proteome of budding yeast Saccharomyces cerevisiae. The units participate in many important cellular processes such as transcription regulation, translation initiation, and mRNA splicing. Within the units, the domains were found to function in a cooperative manner; and each domain contributed to a different aspect of the unit's overall function. The member domains of DASSEM units were found to be significantly enriched among proteins contained in transcription modules, defined as genes sharing similar expression profiles and presumably similar functions. The observation further confirmed the functional coherence of DASSEM units. The functional linkages of units were found in both functionally characterized and uncharacterized proteins and enabled the assessment of protein function based on domain composition. CONCLUSION: A new computational method was developed to identify groups of domains that are linked by a common function in the proteome of Saccharomyces cerevisiae. These groups can either lie within individual proteins or span across different proteins. We propose that the functional linkages among the domains within the DASSEM units can be used as a non-homology based tool to annotate uncharacterized proteins. [Abstract/Link to Full Text]

Moore EB, Poliakov AV, Lincoln P, Brinkley JF
MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data.
BMC Bioinformatics. 2007;8389.
BACKGROUND: Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system. RESULTS: We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: http://sig.biostr.washington.edu/projects/MindSeer. CONCLUSION: MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine. [Abstract/Link to Full Text]

Dundas J, Binkowski TA, DasGupta B, Liang J
Topology independent protein structural alignment.
BMC Bioinformatics. 2007;8388.
BACKGROUND: Identifying structurally similar proteins with different chain topologies can aid studies in homology modeling, protein folding, protein design, and protein evolution. These include circular permuted protein structures, and the more general cases of non-cyclic permutations between similar structures, which are related by non-topological rearrangement beyond circular permutation. We present a method based on an approximation algorithm that finds sequence-order independent structural alignments that are close to optimal. We formulate the structural alignment problem as a special case of the maximum-weight independent set problem, and solve this computationally intensive problem approximately by iteratively solving relaxations of a corresponding integer programming problem. The resulting structural alignment is sequence order independent. Our method is also insensitive to insertions, deletions, and gaps. RESULTS: Using a novel similarity score and a statistical model for significance p-value, we are able to discover previously unknown circular permuted proteins between nucleoplasmin-core protein and auxin binding protein, between aspartate rasemase and 3-dehydrogenate dehydralase, as well as between migration inhibition factor and arginine repressor which involves an additional strand-swapping. We also report the finding of non-cyclic permuted protein structures existing in nature between AML1/core binding factor and ribofalvin synthase. Our method can be used for large scale alignment of protein structures regardless of the topology. CONCLUSION: The approximation algorithm introduced in this work can find good solutions for the problem of protein structure alignment. Furthermore, this algorithm can detect topological differences between two spatially similar protein structures. The alignment between MIF and the arginine repressor demonstrates our algorithm's ability to detect structural similarities even when spatial rearrangement of structural units has occurred. The effectiveness of our method is also demonstrated by the discovery of previously unknown circular permutations. In addition, we report in this study the finding of a naturally occurring non-cyclic permuted protein between AML1/Core Binding Factor chain F and riboflavin synthase chain A. [Abstract/Link to Full Text]

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Recent Articles in Biomedical Digital Libraries

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Recent Articles in Cell Biology Education

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

Fambrough D
Review of: Bio2010: transforming undergraduate education for future research biologists, by the National Research Council. Bio2010: read it!
Cell Biol Educ. 2003;2(2):92-3. [Abstract/Link to Full Text]

Steitz JA
Commentary: Bio2010--new challenges for biology educators.
Cell Biol Educ. 2003;2(2):87-91. [Abstract/Link to Full Text]

Brenner K
Fueling educational reform: Bio2010--biology for the future.
Cell Biol Educ. 2003;2(2):85-6. [Abstract/Link to Full Text]

Blystone R
WWW.Cell Biology Education.
Cell Biol Educ. 2003;2(2):82-4. [Abstract/Link to Full Text]

Allen D, Tanner K
Approaches to cell biology teaching: learning content in context--problem-based learning.
Cell Biol Educ. 2003;2(2):73-81. [Abstract/Link to Full Text]

Bergman L, Schooley C
A successful educational collaboration between scientists and educators: microscopic explorations.
Cell Biol Educ. 2003;2(1):25-8.
The teacher's guide, Microscopic Explorations: A GEMS Festival Guide (Brady and Willard, 1998), is the result of a partnership between Great Explorations in Math and Science (GEMS), a program of the Lawrence Hall of Science (LHS), the public science and curriculum development center of the University of California, Berkeley, and the Microscopy Society of America (MSA). Microscopic Exploration supports the MSA's low-cost national outreach program and, also, reaches a very large educational community as part of the GEMS series. Some of the lessons learned through the extremely successful MSA/LHS collaboration are summarized here in hopes that they may be instructive to other scientists and educators as they launch their own partnerships and collaborations. [Abstract/Link to Full Text]

Tomanek D, Talanquer V, Novodvorsky I, Slater TF
Responding to the call for change: the new college of science teacher preparation program at the university of Arizona.
Cell Biol Educ. 2003;2(1):29-34. [Abstract/Link to Full Text]

Bockholt SM, West JP, Bollenbacher WE
Cancer cell biology: a student-centered instructional module exploring the use of multimedia to enrich interactive, constructivist learning of science.
Cell Biol Educ. 2003;2(1):35-50.
Multimedia has the potential of providing bioscience education novel learning environments and pedagogy applications to foster student interest, involve students in the research process, advance critical thinking/problem-solving skills, and develop conceptual understanding of biological topics. Cancer Cell Biology, an interactive, multimedia, problem-based module, focuses on how mutations in protooncogenes and tumor suppressor genes can lead to uncontrolled cell proliferation by engaging students as research scientists/physicians with the task of diagnosing the molecular basis of tumor growth for a group of patients. The process of constructing the module, which was guided by scientist and student feedback/responses, is described. The completed module and insights gained from its development are presented as a potential "multimedia pedagogy" for the development of other multimedia science learning environments. [Abstract/Link to Full Text]

Griffin V, McMiller T, Jones E, Johnson CM
Identifying novel helix-loop-helix genes in Caenorhabditis elegans through a classroom demonstration of functional genomics.
Cell Biol Educ. 2003;2(1):51-62.
A 14-week, undergraduate-level Genetics and Population Biology course at Morgan State University was modified to include a demonstration of functional genomics in the research laboratory. Students performed a rudimentary sequence analysis of the Caenorhabditis elegans genome and further characterized three sequences that were predicted to encode helix-loop-helix proteins. Students then used reverse transcription-polymerase chain reaction to determine which of the three genes is normally expressed in C. elegans. At the end of this laboratory activity, students were 1) to demonstrate a rudimentary knowledge of bioinformatics, including the ability to differentiate between "having" a gene and "expressing" a gene, and 2) to understand basic approaches to functional genomics, including one specific technique for assaying for gene expression. It was also anticipated that students would increase their skills at effectively communicating their research activities through written and/or oral presentation. This article describes the laboratory activity and the assessment of the effectiveness of the activity. [Abstract/Link to Full Text]

Keiler L, Woolnough B
Students' motivations for data handling choices and behaviors: their explanations of performance.
Cell Biol Educ. 2003;2(1):63-72.
Cries for increased accountability through additional assessment are heard throughout the educational arena. However, as demonstrated in this study, to make a valid assessment of teaching and learning effectiveness, educators must determine not only what students do, but also why they do it, as the latter significantly affects the former. This study describes and analyzes 14- to 16-year-old students' explanations for their choices and performances during science data handling tasks. The study draws heavily on case-study methods for the purpose of seeking an in-depth understanding of classroom processes in an English comprehensive school. During semistructured scheduled and impromptu interviews, students were asked to describe, explain, and justify the work they did with data during their science classes. These student explanations fall within six categories, labeled 1) implementing correct procedures, 2) following instructions, 3) earning marks, 4) doing what is easy, 5) acting automatically, and 6) working within limits. Each category is associated with distinct outcomes for learning and assessment, with some motivations resulting in inflated performances while others mean that learning was underrepresented. These findings illuminate the complexity of student academic choices and behaviors as mediated by an array of motivations, casting doubt on the current understanding of student performance. [Abstract/Link to Full Text]

Labov JB
Education at the National Academies.
Cell Biol Educ. 2003;2(1):6-8. [Abstract/Link to Full Text]

Tanner K, Chatman LS, Allen D
Approaches to cell biology teaching: cooperative learning in the science classroom--beyond students working in groups.
Cell Biol Educ. 2003;2(1):1-5. [Abstract/Link to Full Text]

Wright R, Boggs J
Learning cell biology as a team: a project-based approach to upper-division cell biology.
Cell Biol Educ. 2002;1(4):145-53.
To help students develop successful strategies for learning how to learn and communicate complex information in cell biology, we developed a quarter-long cell biology class based on team projects. Each team researches a particular human disease and presents information about the cellular structure or process affected by the disease, the cellular and molecular biology of the disease, and recent research focused on understanding the cellular mechanisms of the disease process. To support effective teamwork and to help students develop collaboration skills useful for their future careers, we provide training in working in small groups. A final poster presentation, held in a public forum, summarizes what students have learned throughout the quarter. Although student satisfaction with the course is similar to that of standard lecture-based classes, a project-based class offers unique benefits to both the student and the instructor. [Abstract/Link to Full Text]

Gladfelter A
A lab with a view: American postdocs abroad.
Cell Biol Educ. 2002;1(4):128-31. [Abstract/Link to Full Text]

Dyer BD, LeBlanc MD
Meeting report: Incorporating genomics research into undergraduate curricula.
Cell Biol Educ. 2002;1(4):101-4. [Abstract/Link to Full Text]

Fink RD
Cloning, stem cells, and the current national debate: incorporating ethics into a large introductory biology course.
Cell Biol Educ. 2002;1(4):132-44.
Discussing the ethical issues involved in topics such as cloning and stem cell research in a large introductory biology course is often difficult. Teachers may be wary of presenting material biased by personal beliefs, and students often feel inhibited speaking about moral issues in a large group. Yet, to ignore what is happening "out there" beyond the textbooks and lab work is to do a disservice to students. This essay describes a semester-long project in which upperclass students presented some of the most complex and controversial ideas imaginable to introductory students by staging a mock debate and acting as members of the then newly appointed President's Council on Bioethics. Because the upperclass students were presenting the ideas of real people who play an important role in shaping national policy, no student's personal beliefs were put on the line, and many ideas were articulated. The introductory audience could accept or reject what they were hearing and learn information important for making up their own minds on these issues. This project is presented as an example of how current events can be used to put basic cell biology into context and of how exciting it can be when students teach students. [Abstract/Link to Full Text]

DebBurman SK
Learning how scientists work: experiential research projects to promote cell biology learning and scientific process skills.
Cell Biol Educ. 2002;1(4):154-72.
Facilitating not only the mastery of sophisticated subject matter, but also the development of process skills is an ongoing challenge in teaching any introductory undergraduate course. To accomplish this goal in a sophomore-level introductory cell biology course, I require students to work in groups and complete several mock experiential research projects that imitate the professional activities of the scientific community. I designed these projects as a way to promote process skill development within content-rich pedagogy and to connect text-based and laboratory-based learning with the world of contemporary research. First, students become familiar with one primary article from a leading peer-reviewed journal, which they discuss by means of PowerPoint-based journal clubs and journalism reports highlighting public relevance. Second, relying mostly on primary articles, they investigate the molecular basis of a disease, compose reviews for an in-house journal, and present seminars in a public symposium. Last, students author primary articles detailing investigative experiments conducted in the lab. This curriculum has been successful in both quarter-based and semester-based institutions. Student attitudes toward their learning were assessed quantitatively with course surveys. Students consistently reported that these projects significantly lowered barriers to primary literature, improved research-associated skills, strengthened traditional pedagogy, and helped accomplish course objectives. Such approaches are widely suited for instructors seeking to integrate process with content in their courses. [Abstract/Link to Full Text]

Vallen E
Analysis of protein localization and secretory pathway function using the yeast Saccharomyces cerevisiae.
Cell Biol Educ. 2002;1(4):173-92.
The isolation and characterization of mutants has been crucial in understanding a number of processes in the field of cell biology. In this exercise, students examine the effects of mutations in the secretory pathway on protein localization. Yeast strains deficient for synthesis of histidinol dehydrogenase are transformed with a plasmid encoding a chimeric protein. The chimera contains a signal sequence fused to histidinol dehydrogenase. A strain with a defect in the translocation of secretory proteins into the endoplasmic reticulum (ER) accumulates sufficient histidinol dehydrogenase in the cytoplasm to grow on media lacking histidine. In contrast, yeast proficient for secretion, or yeast with secretion defects later in the pathway, are unable to grow on media lacking histidine. Student analysis of the experimental yeast transformants and appropriate controls allows investigation into the effects of conditional defects in the secretory pathway on both cell viability and protein localization. The exercise is usually performed in a manner that allows students to execute a number of techniques common in molecular biology laboratories, including plasmid minipreps, restriction digestions, and Southern blots. Student understanding and enjoyment of the exercise was assessed by laboratory reports, oral and written examinations, and questionnaires. After completion of these experiments, students can describe the utility of protein fusions, the roles of mutant analysis in cell biology, and the steps taken by proteins transiting the secretory pathway. [Abstract/Link to Full Text]

Wilson DJ, Haynes JK
ASCB Minorities Affairs Committee goals: "strengthening the chain of success".
Cell Biol Educ. 2002;1(4):105-6. [Abstract/Link to Full Text]

Wood WB
Advanced high school biology in an era of rapid change: a summary of the biology panel report from the NRC Committee on Programs for Advanced Study of Mathematics and Science in American High Schools.
Cell Biol Educ. 2002;1(4):123-7.
A recently released National Research Council (NRC) report, Learning and Understanding: Improving Advanced Study of Mathematics and Science in U.S. High Schools, evaluated and recommended changes in the Advanced Placement (AP), International Baccalaureate (IB), and other advanced secondary school science programs. As part of this study, discipline-specific panels were formed to evaluate advanced programs in biology, chemistry, physics, and mathematics. Among the conclusions of the Content Panel for Biology were that AP courses in particular suffer from inadequate quality control as well as excessive pressure to fulfill their advanced placement function, which encourages teachers to attempt coverage of all areas of biology and emphasize memorization of facts rather than in-depth understanding. In this essay, the Panel's principal findings are discussed, with an emphasis on its recommendation that colleges and universities should be strongly discouraged from using performance on either the AP examination or the IB examination as the sole basis for automatic placement out of required introductory courses for biology majors and distribution requirements for nonmajors. [Abstract/Link to Full Text]

Alberts B
From the National Academies.
Cell Biol Educ. 2002;1(4):109-10. [Abstract/Link to Full Text]

Barkanic S
Fueling educational reform: the HHMI professors.
Cell Biol Educ. 2002;1(4):107-8. [Abstract/Link to Full Text]

Tanner K, Allen D
Approaches to cell biology teaching: a primer on standards.
Cell Biol Educ. 2002;1(4):95-100. [Abstract/Link to Full Text]

Labov JB
National and state standards in science and their potential influence on undergraduate science education.
CBE Life Sci Educ. 2006;5(3):204-9. [Abstract/Link to Full Text]

Odom DP, Grossel MJ
Using the two-hybrid screen in the classroom laboratory.
Cell Biol Educ. 2002;1(1):43-62.
The National Science Foundation and others have made compelling arguments that research be incorporated into the learning of undergraduates. In response to these arguments, a two-hybrid research project was incorporated into a molecular biology course that contained both a lecture section and a laboratory section. The course was designed around specific goals for educational outcomes, including introducing research to a wide range of students, teaching students experimental design and data analysis, and enhancing understanding of course material. Additional goals included teaching students to search genomic databases, to access scientific articles, and to write a paper in scientific format. Graded events tested these goals, and a student evaluation indicated student perception of the project. According to our analysis of the data, the yeast two-hybrid screen was a success: several novel clones were identified; students met expectations on graded lab reports, the poster session, and the final paper; and evaluations indicated that students had achieved the outlined goals. Students indicated on the evaluations that the research project increased their interest in research and greatly improved understanding of the course material. Finally, several students in the course intend to submit the findings of the research project to an undergraduate research journal. [Abstract/Link to Full Text]

Lewis JR, Kotur MS, Butt O, Kulcarni S, Riley AA, Ferrell N, Sullivan KD, Ferrari M
Biotechnology apprenticeship for secondary-level students: teaching advanced cell culture techniques for research.
Cell Biol Educ. 2002;1(1):26-42.
The purpose of this article is to discuss small-group apprenticeships (SGAs) as a method to instruct cell culture techniques to high school participants. The study aimed to teach cell culture practices and to introduce advanced imaging techniques to solve various biomedical engineering problems. Participants designed and completed experiments using both flow cytometry and laser scanning cytometry during the 1-month summer apprenticeship. In addition to effectively and efficiently teaching cell biology laboratory techniques, this course design provided an opportunity for research training, career exploration, and mentoring. Students participated in active research projects, working with a skilled interdisciplinary team of researchers in a large research institution with access to state-of-the-art instrumentation. The instructors, composed of graduate students, laboratory managers, and principal investigators, worked well together to present a real and worthwhile research experience. The students enjoyed learning cell culture techniques while contributing to active research projects. The institution's researchers were equally enthusiastic to instruct and serve as mentors. In this article, we clarify and illuminate the value of small-group laboratory apprenticeships to the institution and the students by presenting the results and experiences of seven middle and high school participants and their instructors. [Abstract/Link to Full Text]

Sundberg MD
Assessing student learning.
Cell Biol Educ. 2002;1(1):11-5.
Biology education research has now reached a level of maturity where the expectation is that researchers will assess the effectiveness of their innovation on student learning. This may include an examination of affective outcomes, such as student attitudes and beliefs, as well as student understanding of discipline-based content. A variety of tools are available to generate assessment data, each with certain advantages and disadvantages. They include not only quantitative measures, which lend themselves to familiar statistical analyses, but also qualitative techniques that can provide a rich understanding of complex outcomes. This article describes some of the most commonly used assessment techniques, their advantages and disadvantages, and typical ways such information is reported. [Abstract/Link to Full Text]

Watters C
Video views and reviews.
Cell Biol Educ. 2002;1(1):6-7. [Abstract/Link to Full Text]

Elgin S
Report from the ASCB Education Committee.
Cell Biol Educ. 2002;1(1):8. [Abstract/Link to Full Text]

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

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

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Recent Articles in BMC Medical Informatics and Decision Making

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Aziz O, Panesar SS, Netuveli G, Paraskeva P, Sheikh A, Darzi A
Handheld computers and the 21st century surgical team: a pilot study.
BMC Med Inform Decis Mak. 2005;528.
BACKGROUND: The commercial development and expansion of mobile phone networks has led to the creation of devices combining mobile phones and personal digital assistants, which could prove invaluable in a clinical setting. This pilot study aimed to look at how one such device compared with the current pager system in facilitating inter-professional communication in a hospital clinical team. METHODS: The study looked at a heterogeneous team of doctors (n = 9) working in a busy surgical setting at St. Mary's Hospital in London and compared the use of a personal digital assistant with mobile phone and web-browsing facilities to the existing pager system. The primary feature of this device being compared to the conventional pager was its use as a mobile phone, but other features evaluated included the ability to access the internet, and reference data on the device. A crossover study was carried out for 6 weeks in 2004, with the team having access to the personal digital assistant every alternate week. The primary outcome measure for assessing efficiency of communication was the length of time it took for clinicians to respond to a call. We also sought to assess the ease of adoption of new technology by evaluating the perceptions of the team (n = 9) to personal digital assistants, by administering a questionnaire. RESULTS: Doctors equipped with a personal digital assistant rather than a pager, responded more quickly to a call and had a lower of failure to respond rate (RR: 0.44; 95%CI 0.20-0.93). Clinicians also found this technology easy to adopt as seen by a significant reduction in perceptions of nervousness to the technology over the six-week study period (mean (SD) week 1: 4.10 (SD 1.69) vs. mean (SD) week 6: 2.20 (1.99); p = 0.04). CONCLUSION: The results of this pilot study show the possible effects of replacing the current hospital pager with a newer, more technologically advanced device, and suggest that a combined personal digital assistant and mobile phone device may improve communication between doctors. In the light of these encouraging preliminary findings, we propose a large-scale clinical trial of the use of these devices in facilitating inter-professional communication in a hospital setting. [Abstract/Link to Full Text]

Doyle TJ, Ma H, Groseclose SL, Hopkins RS
PHSkb: a knowledgebase to support notifiable disease surveillance.
BMC Med Inform Decis Mak. 2005;527.
BACKGROUND: Notifiable disease surveillance in the United States is predominantly a passive process that is often limited by poor timeliness and low sensitivity. Interoperable tools are needed that interact more seamlessly with existing clinical and laboratory data to improve notifiable disease surveillance. DESCRIPTION: The Public Health Surveillance Knowledgebase (PHSkb) is a computer database designed to provide quick, easy access to domain knowledge regarding notifiable diseases and conditions in the United States. The database was developed using Protégé ontology and knowledgebase editing software. Data regarding the notifiable disease domain were collected via a comprehensive review of state health department websites and integrated with other information used to support the National Notifiable Diseases Surveillance System (NNDSS). Domain concepts were harmonized, wherever possible, to existing vocabulary standards. The knowledgebase can be used: 1) as the basis for a controlled vocabulary of reportable conditions needed for data aggregation in public health surveillance systems; 2) to provide queriable domain knowledge for public health surveillance partners; 3) to facilitate more automated case detection and surveillance decision support as a reusable component in an architecture for intelligent clinical, laboratory, and public health surveillance information systems. CONCLUSIONS: The PHSkb provides an extensible, interoperable system architecture component to support notifiable disease surveillance. Further development and testing of this resource is needed. [Abstract/Link to Full Text]

Kline JA, Johnson CL, Pollack CV, Diercks DB, Hollander JE, Newgard CD, Garvey JL
Pretest probability assessment derived from attribute matching.
BMC Med Inform Decis Mak. 2005;526.
BACKGROUND: Pretest probability (PTP) assessment plays a central role in diagnosis. This report compares a novel attribute-matching method to generate a PTP for acute coronary syndrome (ACS). We compare the new method with a validated logistic regression equation (LRE). METHODS: Eight clinical variables (attributes) were chosen by classification and regression tree analysis of a prospectively collected reference database of 14,796 emergency department (ED) patients evaluated for possible ACS. For attribute matching, a computer program identifies patients within the database who have the exact profile defined by clinician input of the eight attributes. The novel method was compared with the LRE for ability to produce PTP estimation <2% in a validation set of 8,120 patients evaluated for possible ACS and did not have ST segment elevation on ECG. 1,061 patients were excluded prior to validation analysis because of ST-segment elevation (713), missing data (77) or being lost to follow-up (271). RESULTS: In the validation set, attribute matching produced 267 unique PTP estimates [median PTP value 6%, 1st-3rd quartile 1-10%] compared with the LRE, which produced 96 unique PTP estimates [median 24%, 1st-3rd quartile 10-30%]. The areas under the receiver operating characteristic curves were 0.74 (95% CI 0.65 to 0.82) for the attribute matching curve and 0.68 (95% CI 0.62 to 0.77) for LRE. The attribute matching system categorized 1,670 (24%, 95% CI = 23-25%) patients as having a PTP < 2.0%; 28 developed ACS (1.7% 95% CI = 1.1-2.4%). The LRE categorized 244 (4%, 95% CI = 3-4%) with PTP < 2.0%; four developed ACS (1.6%, 95% CI = 0.4-4.1%). CONCLUSION: Attribute matching estimated a very low PTP for ACS in a significantly larger proportion of ED patients compared with a validated LRE. [Abstract/Link to Full Text]

Nohle DG, Hackman BA, Ayers LW
The tissue micro-array data exchange specification: a web based experience browsing imported data.
BMC Med Inform Decis Mak. 2005;525.
BACKGROUND: The AIDS and Cancer Specimen Resource (ACSR) is an HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers to approved researchers HIV infected biologic samples and uninfected control tissues including tissue cores in micro-arrays (TMA) accompanied by de-identified clinical data. Researchers interested in the type and quality of TMA tissue cores and the associated clinical data need an efficient method for viewing available TMA materials. Because each of the tissue samples within a TMA has separate data including a core tissue digital image and clinical data, an organized, standard approach to producing, navigating and publishing such data is necessary. The Association for Pathology Informatics (API) extensible mark-up language (XML) TMA data exchange specification (TMA DES) proposed in April 2003 provides a common format for TMA data. Exporting TMA data into the proposed format offers an opportunity to implement the API TMA DES. Using our public BrowseTMA tool, we created a web site that organizes and cross references TMA lists, digital "virtual slide" images, TMA DES export data, linked legends and clinical details for researchers. Microsoft Excel and Microsoft Word are used to convert tabular clinical data and produce an XML file in the TMA DES format. The BrowseTMA tool contains Extensible Stylesheet Language Transformation (XSLT) scripts that convert XML data into Hyper-Text Mark-up Language (HTML) web pages with hyperlinks automatically added to allow rapid navigation. RESULTS: Block lists, virtual slide images, legends, clinical details and exports have been placed on the ACSR web site for 14 blocks with 1623 cores of 2.0, 1.0 and 0.6 mm sizes. Our virtual microscope can be used to view and annotate these TMA images. Researchers can readily navigate from TMA block lists to TMA legends and to clinical details for a selected tissue core. Exports for 11 blocks with 3812 cores from three other institutions were processed with the BrowseTMA tool. Fifty common data elements (CDE) from the TMA DES were used and 42 more created for site-specific data. Researchers can download TMA clinical data in the TMA DES format. CONCLUSION: Virtual TMAs with clinical data can be viewed on the Internet by interested researchers using the BrowseTMA tool. We have organized our approach to producing, sorting, navigating and publishing TMA information to facilitate such review. We have converted Excel TMA data into TMA DES XML, and imported it and TMA DES XML from another institution into BrowseTMA to produce web pages that allow us to browse through the merged data. We proposed enhancements to the TMA DES as a result of this experience. We implemented improvements to the API TMA DES as a result of using exported data from several institutions. A document type definition was written for the API TMA DES (that optionally includes proposed enhancements). Independent validators can be used to check exports against the DTD (with or without the proposed enhancements). Linking tissue core images to readily navigable clinical data greatly improves the value of the TMA. [Abstract/Link to Full Text]

Waruru AK, Nduati R, Tylleskär T
Audio computer-assisted self-interviewing (ACASI) may avert socially desirable responses about infant feeding in the context of HIV.
BMC Med Inform Decis Mak. 2005;524.
BACKGROUND: Understanding infant feeding practices in the context of HIV and factors that put mothers at risk of HIV infection is an important step towards prevention of mother to child transmission of HIV (PMTCT). Face-to-face (FTF) interviewing may not be a suitable way of ascertaining this information because respondents may report what is socially desirable. Audio computer-assisted self-interviewing (ACASI) is thought to increase privacy, reporting of sensitive issues and to eliminate socially desirable responses. We compared ACASI with FTF interviewing and explored its feasibility, usability, and acceptability in a PMTCT program in Kenya. METHODS: A graphic user interface (GUI) was developed using Macromedia Authorware and questions and instructions recorded in local languages Kikuyu and Kiswahili. Eighty mothers enrolled in the PMTCT program were interviewed with each of the interviewing mode (ACASI and FTF) and responses obtained in FTF interviews and ACASI compared using McNemar's chi2 for paired proportions. A paired Student's t-test was used to compare means of age, marital-time and parity when measuring interview mode effect and two-sample Student's t-test to compare means for samples stratified by education level - determined during the exit interview. A Chi-Square (chi2test) was used to compare ability to use ACASI by education level. RESULTS: Mean ages for intended time for breastfeeding as reported by ACASI were 11 months by ACASI and 19 months by FTF interviewing (p < 0.001). Introduction of complementary foods at <or=3 months was reported more frequently by respondents in ACASI compared to FTF interviews for 7 of 13 complementary food items commonly utilized in the study area (p < 0.05). More respondents reported use of unsuitable utensils for infant feeding in ACASI than in FTF interviewing (p = 0.001). In other sensitive questions, 7% more respondents reported unstable relationships with ACASI than when interviewed FTF (p = 0.039). Regardless of education level, respondents used ACASI similarly and majority (65%) preferred it to FTF interviewing mainly due to enhanced usability and privacy. Most respondents (79%) preferred ACASI to FTF for future interviewing. CONCLUSION: ACASI seems to improve quality of information by increasing response to sensitive questions, decreasing socially desirable responses, and by preventing null responses and was suitable for collecting data in a setting where formal education is low. [Abstract/Link to Full Text]

Shiffman RN, Dixon J, Brandt C, Essaihi A, Hsiao A, Michel G, O'Connell R
The GuideLine Implementability Appraisal (GLIA): development of an instrument to identify obstacles to guideline implementation.
BMC Med Inform Decis Mak. 2005;523.
BACKGROUND: Clinical practice guidelines are not uniformly successful in influencing clinicians' behaviour toward best practices. Implementability refers to a set of characteristics that predict ease of (and obstacles to) guideline implementation. Our objective is to develop and validate a tool for appraisal of implementability of clinical guidelines. METHODS: Indicators of implementability were identified from the literature and used to create items and dimensions of the GuideLine Implementability Appraisal (GLIA). GLIA consists of 31 items, arranged into 10 dimensions. Questions from 9 of the 10 dimensions are applied individually to each recommendation of the guideline. Decidability and Executability are critical dimensions. Other dimensions are Global, Presentation and Formatting, Measurable Outcomes, Apparent Validity, Flexibility, Effect on Process of Care, Novelty/Innovation, and Computability. We conducted a series of validation activities, including validation of the construct of implementability, expert review of content for clarity, relevance, and comprehensiveness, and assessment of construct validity of the instrument. Finally, GLIA was applied to a draft guideline under development by national professional societies. RESULTS: Evidence of content validity and preliminary support for construct validity were obtained. The GLIA proved to be useful in identifying barriers to implementation in the draft guideline and the guideline was revised accordingly. CONCLUSION: GLIA may be useful to guideline developers who can apply the results to remedy defects in their guidelines. Likewise, guideline implementers may use GLIA to select implementable recommendations and to devise implementation strategies that address identified barriers. By aiding the design and operationalization of highly implementable guidelines, our goal is that application of GLIA may help to improve health outcomes, but further evaluation will be required to support this potential benefit. [Abstract/Link to Full Text]

Cassa CA, Iancu K, Olson KL, Mandl KD
A software tool for creating simulated outbreaks to benchmark surveillance systems.
BMC Med Inform Decis Mak. 2005;522.
BACKGROUND: Evaluating surveillance systems for the early detection of bioterrorism is particularly challenging when systems are designed to detect events for which there are few or no historical examples. One approach to benchmarking outbreak detection performance is to create semi-synthetic datasets containing authentic baseline patient data (noise) and injected artificial patient clusters, as signal. METHODS: We describe a software tool, the AEGIS Cluster Creation Tool (AEGIS-CCT), that enables users to create simulated clusters with controlled feature sets, varying the desired cluster radius, density, distance, relative location from a reference point, and temporal epidemiological growth pattern. AEGIS-CCT does not require the use of an external geographical information system program for cluster creation. The cluster creation tool is an open source program, implemented in Java and is freely available under the Lesser GNU Public License at its Sourceforge website. Cluster data are written to files or can be appended to existing files so that the resulting file will include both existing baseline and artificially added cases. Multiple cluster file creation is an automated process in which multiple cluster files are created by varying a single parameter within a user-specified range. To evaluate the output of this software tool, sets of test clusters were created and graphically rendered. RESULTS: Based on user-specified parameters describing the location, properties, and temporal pattern of simulated clusters, AEGIS-CCT created clusters accurately and uniformly. CONCLUSION: AEGIS-CCT enables the ready creation of datasets for benchmarking outbreak detection systems. It may be useful for automating the testing and validation of spatial and temporal cluster detection algorithms. [Abstract/Link to Full Text]

Väliaho J, Riikonen P, Vihinen M
Distribution of immunodeficiency fact files with XML--from Web to WAP.
BMC Med Inform Decis Mak. 2005;521.
BACKGROUND: Although biomedical information is growing rapidly, it is difficult to find and retrieve validated data especially for rare hereditary diseases. There is an increased need for services capable of integrating and validating information as well as proving it in a logically organized structure. A XML-based language enables creation of open source databases for storage, maintenance and delivery for different platforms. METHODS: Here we present a new data model called fact file and an XML-based specification Inherited Disease Markup Language (IDML), that were developed to facilitate disease information integration, storage and exchange. The data model was applied to primary immunodeficiencies, but it can be used for any hereditary disease. Fact files integrate biomedical, genetic and clinical information related to hereditary diseases. RESULTS: IDML and fact files were used to build a comprehensive Web and WAP accessible knowledge base ImmunoDeficiency Resource (IDR) available at http://bioinf.uta.fi/idr/. A fact file is a user oriented user interface, which serves as a starting point to explore information on hereditary diseases. CONCLUSION: The IDML enables the seamless integration and presentation of genetic and disease information resources in the Internet. IDML can be used to build information services for all kinds of inherited diseases. The open source specification and related programs are available at http://bioinf.uta.fi/idml/. [Abstract/Link to Full Text]

Wilczynski NL, Morgan D, Haynes RB
An overview of the design and methods for retrieving high-quality studies for clinical care.
BMC Med Inform Decis Mak. 2005;520.
BACKGROUND: With the information explosion, the retrieval of the best clinical evidence from large, general purpose, bibliographic databases such as MEDLINE can be difficult. Both researchers conducting systematic reviews and clinicians faced with a patient care question are confronted with the daunting task of searching for the best medical literature in electronic databases. Many have advocated the use of search filters or "hedges" to assist with the searching process. The purpose of this report is to describe the design and methods of a study that set out to develop optimal search strategies for retrieving sound clinical studies of health disorders in large electronics databases. OBJECTIVE: To describe the design and methods of a study that set out to develop optimal search strategies for retrieving sound clinical studies of health disorders in large electronic databases. DESIGN: An analytic survey comparing hand searches of 170 journals in the year 2000 with retrievals from MEDLINE, EMBASE, CINAHL, and PsycINFO for candidate search terms and combinations. The sensitivity, specificity, precision, and accuracy of unique search terms and combinations of search terms were calculated. CONCLUSION: A study design modeled after a diagnostic testing procedure with a gold standard (the hand search of the literature) and a test (the search terms) is an effective way of developing, testing, and validating search strategies for use in large electronic databases. [Abstract/Link to Full Text]

Olson KL, Bonetti M, Pagano M, Mandl KD
Real time spatial cluster detection using interpoint distances among precise patient locations.
BMC Med Inform Decis Mak. 2005;519.
BACKGROUND: Public health departments in the United States are beginning to gain timely access to health data, often as soon as one day after a visit to a health care facility. Consequently, new approaches to outbreak surveillance are being developed. When cases cluster geographically, an analysis of their spatial distribution can facilitate outbreak detection. Our method focuses on detecting perturbations in the distribution of pair-wise distances among all patients in a geographical region. Barring outbreaks, this distribution can be quite stable over time. We sought to exemplify the method by measuring its cluster detection performance, and to determine factors affecting sensitivity to spatial clustering among patients presenting to hospital emergency departments with respiratory syndromes. METHODS: The approach was to (1) define a baseline spatial distribution of home addresses for a population of patients visiting an emergency department with respiratory syndromes using historical data; (2) develop a controlled feature set simulation by inserting simulated outbreak data with varied parameters into authentic background noise, thereby creating semisynthetic data; (3) compare the observed with the expected spatial distribution; (4) establish the relative value of different alarm strategies so as to maximize sensitivity for the detection of clustering; and (5) measure factors which have an impact on sensitivity. RESULTS: Overall sensitivity to detect spatial clustering was 62%. This contrasts with an overall alarm rate of less than 5% for the same number of extra visits when the extra visits were not characterized by geographic clustering. Clusters that produced the least number of alarms were those that were small in size (10 extra visits in a week, where visits per week ranged from 120 to 472), diffusely distributed over an area with a 3 km radius, and located close to the hospital (5 km) in a region most densely populated with patients to this hospital. Near perfect alarm rates were found for clusters that varied on the opposite extremes of these parameters (40 extra visits, within a 250 meter radius, 50 km from the hospital). CONCLUSION: Measuring perturbations in the interpoint distance distribution is a sensitive method for detecting spatial clustering. When cases are clustered geographically, there is clearly power to detect clustering when the spatial distribution is represented by the M statistic, even when clusters are small in size. By varying independent parameters of simulated outbreaks, we have demonstrated empirically the limits of detection of different types of outbreaks. [Abstract/Link to Full Text]

Valaitis RK, Akhtar-Danesh N, Kealey CM, Brunetti GM, Thomas H
A Severe Acute Respiratory Syndrome Extranet: supporting local communication and information dissemination.
BMC Med Inform Decis Mak. 2005;5(1):17.
BACKGROUND: The objective of this study was to explore the use and perceptions of a local Severe Acute Respiratory Syndrome (SARS) Extranet and its potential to support future information and communication applications. The SARS Extranet was a single, managed electronic and limited access system to manage local, provincial and other SARS control information. METHODS: During July, 2003, a web-based and paper-based survey was conducted with 53 SARS Steering Committee members in Hamilton. It assessed the use and perceptions of the Extranet that had been built to support the committee during the SARS outbreak. Before distribution, the survey was user-tested based on a think-aloud protocol, and revisions were made. Quantitative and qualitative questions were asked related to frequency of use of the Extranet, perceived overall usefulness of the resource, rationale for use, potential barriers, strengths and limitations, and potential future uses of the Extranet. RESULTS: The response rate was 69.4% (n = 34). Of all respondents, 30 (88.2%) reported that they had visited the site, and rated it highly overall (mean = 4.0; 1 = low to 5 = high). However, the site was rated 3.4 compared with other communications strategies used during the outbreak. Almost half of all respondents (44.1%) visited the site at least once every few days. The two most common reasons the 30 respondents visited the Extranet were to access SARS Steering Committee minutes (63.3%) and to access Hamilton medical advisories (53.3%). The most commonly cited potential future uses for the Extranet were the sending of private emails to public health experts (63.3%), and surveillance (63.3%). No one encountered personal barriers in his or her use of the site, but several mentioned that time and duplication of email information were challenges. CONCLUSION: Despite higher rankings of various communication strategies during the SARS outbreak, such as email, meetings, teleconferences, and other web sites, users generally perceived a local Extranet as a useful support for the dissemination of local information during public health emergencies. [Abstract/Link to Full Text]

Sibert L, Darmoni SJ, Dahamna B, Weber J, Charlin B
Online clinical reasoning assessment with the Script Concordance test: a feasibility study.
BMC Med Inform Decis Mak. 2005;518.
BACKGROUND: The script concordance (SC) test is an assessment tool that measures capacity to solve ill-defined problems, that is, reasoning in context of uncertainty. This tool has been used up to now mainly in medicine. The purpose of this pilot study is to assess the feasibility of the test delivered on the Web to French urologists. METHODS: The principle of SC test construction and the development of the Web site are described. A secure Web site was created with two sequential modules: (a) The first one for the reference panel (n = 26) with two sub-tasks: to validate the content of the test and to elaborate the scoring system; (b) The second for candidates with different levels of experience in Urology: Board certified urologists, residents, medical students (5 or 6th year). Minimum expected number of participants is 150 for urologists, 100 for residents and 50 for medical students. Each candidate is provided with an individual access code to this Web site. He/she may complete the Script Concordance test several times during his/her curriculum. RESULTS: The Web site has been operational since April 2004. The reference panel validated the test in June of the same year during the annual seminar of the French Society of Urology. The Web site is available for the candidates since September 2004. In six months, 80% of the target figure for the urologists, 68% of the target figure for the residents and 20% of the target figure for the student passed the test online. During these six months, no technical problem was encountered. CONCLUSION: The feasibility of the web-based SC test is successful as two-thirds of the expected number of participants was included within six months. Psychometric properties (validity, reliability) of the test will be evaluated on a large scale (N = 300). If positive, educational impact of this assessment tool will be useful to help urologists during their curriculum for the acquisition of clinical reasoning skills, which is crucial for professional competence. [Abstract/Link to Full Text]

Holmes-Rovner M, Stableford S, Fagerlin A, Wei JT, Dunn RL, Ohene-Frempong J, Kelly-Blake K, Rovner DR
Evidence-based patient choice: a prostate cancer decision aid in plain language.
BMC Med Inform Decis Mak. 2005;5(1):16.
BACKGROUND: Decision aids (DA) to assist patients in evaluating treatment options and sharing in decision making have proliferated in recent years. Most require high literacy and do not use plain language principles. We describe one of the first attempts to design a decision aid using principles from reading research and document design. The plain language DA prototype addressed treatment decisions for localized prostate cancer. Evaluation assessed impact on knowledge, decisions, and discussions with doctors in men newly diagnosed with prostate cancer. METHODS: Document development steps included preparing an evidence-based DA in standard medical parlance, iteratively translating it to emphasize shared decision making and plain language in three formats (booklet, Internet, and audio-tape). Scientific review of medical content was integrated with expert health literacy review of document structure and design. Formative evaluation methods included focus groups (n = 4) and survey of a new sample of men newly diagnosed with prostate cancer (n = 60), compared with historical controls (n = 184). RESULTS: A transparent description of the development process and design elements is reported. Formative evaluation among newly diagnosed prostate cancer patients found the DA to be clear and useful in reaching a decision. Newly diagnosed patients reported more discussions with doctors about treatment options, and showed increases in knowledge of side effects of radiation therapy. CONCLUSION: The plain language DA presenting medical evidence in text and numerical formats appears acceptable and useful in decision-making about localized prostate cancer treatment. Further testing should evaluate the impact of all three media on decisions made and quality of life in the survivorship period, especially among very low literacy men. [Abstract/Link to Full Text]

Pietrobon R, Nielsen KC, Steele SM, Menezes AP, Martins H, Jacobs DO
Manuscript Architect: a Web application for scientific writing in virtual interdisciplinary groups.
BMC Med Inform Decis Mak. 2005;5(1):15.
BACKGROUND: Although scientific writing plays a central role in the communication of clinical research findings and consumes a significant amount of time from clinical researchers, few Web applications have been designed to systematically improve the writing process.This application had as its main objective the separation of the multiple tasks associated with scientific writing into smaller components. It was also aimed at providing a mechanism where sections of the manuscript (text blocks) could be assigned to different specialists. Manuscript Architect was built using Java language in conjunction with the classic lifecycle development method. The interface was designed for simplicity and economy of movements. Manuscripts are divided into multiple text blocks that can be assigned to different co-authors by the first author. Each text block contains notes to guide co-authors regarding the central focus of each text block, previous examples, and an additional field for translation when the initial text is written in a language different from the one used by the target journal. Usability was evaluated using formal usability tests and field observations. RESULTS: The application presented excellent usability and integration with the regular writing habits of experienced researchers. Workshops were developed to train novice researchers, presenting an accelerated learning curve. The application has been used in over 20 different scientific articles and grant proposals. CONCLUSION: The current version of Manuscript Architect has proven to be very useful in the writing of multiple scientific texts, suggesting that virtual writing by interdisciplinary groups is an effective manner of scientific writing when interdisciplinary work is required. [Abstract/Link to Full Text]

Sittig DF, Shiffman RN, Leonard K, Friedman C, Rudolph B, Hripcsak G, Adams LL, Kleinman LC, Kaushal R
A draft framework for measuring progress towards the development of a National Health Information Infrastructure.
BMC Med Inform Decis Mak. 2005;5(1):14.
BACKGROUND: American public policy makers recently established the goal of providing the majority of Americans with electronic health records by 2014. This will require a National Health Information Infrastructure (NHII) that is far more complete than the one that is currently in its formative stage of development. We describe a conceptual framework to help measure progress toward that goal. DISCUSSION: The NHII comprises a set of clusters, such as Regional Health Information Organizations (RHIOs), which, in turn, are composed of smaller clusters and nodes such as private physician practices, individual hospitals, and large academic medical centers. We assess progress in terms of the availability and use of information and communications technology and the resulting effectiveness of these implementations. These three attributes can be studied in a phased approach because the system must be available before it can be used, and it must be used to have an effect. As the NHII expands, it can become a tool for evaluating itself. SUMMARY: The NHII has the potential to transform health care in America--improving health care quality, reducing health care costs, preventing medical errors, improving administrative efficiencies, reducing paperwork, and increasing access to affordable health care. While the President has set an ambitious goal of assuring that most Americans have electronic health records within the next 10 years, a significant question remains "How will we know if we are making progress toward that goal?" Using the definitions for "nodes" and "clusters" developed in this article along with the resulting measurement framework, we believe that we can begin a discussion that will enable us to define and then begin making the kinds of measurements necessary to answer this important question. [Abstract/Link to Full Text]

Elkin PL, Brown SH, Bauer BA, Husser CS, Carruth W, Bergstrom LR, Wahner-Roedler DL
A controlled trial of automated classification of negation from clinical notes.
BMC Med Inform Decis Mak. 2005;5(1):13.
BACKGROUND: Identification of negation in electronic health records is essential if we are to understand the computable meaning of the records: Our objective is to compare the accuracy of an automated mechanism for assignment of Negation to clinical concepts within a compositional expression with Human Assigned Negation. Also to perform a failure analysis to identify the causes of poorly identified negation (i.e. Missed Conceptual Representation, Inaccurate Conceptual Representation, Missed Negation, Inaccurate identification of Negation). METHODS: 41 Clinical Documents (Medical Evaluations; sometimes outside of Mayo these are referred to as History and Physical Examinations) were parsed using the Mayo Vocabulary Server Parsing Engine. SNOMED-C was used to provide concept coverage for the clinical concepts in the record. These records resulted in identification of Concepts and textual clues to Negation. These records were reviewed by an independent medical terminologist, and the results were tallied in a spreadsheet. Where questions on the review arose Internal Medicine Faculty were employed to make a final determination. RESULTS: SNOMED-CT was used to provide concept coverage of the 14,792 Concepts in 41 Health Records from John's Hopkins University. Of these, 1,823 Concepts were identified as negative by Human review. The sensitivity (Recall) of the assignment of negation was 97.2% (p < 0.001, Pearson Chi-Square test; when compared to a coin flip). The specificity of assignment of negation was 98.8%. The positive likelihood ratio of the negation was 81. The positive predictive value (Precision) was 91.2% CONCLUSION: Automated assignment of negation to concepts identified in health records based on review of the text is feasible and practical. Lexical assignment of negation is a good test of true Negativity as judged by the high sensitivity, specificity and positive likelihood ratio of the test. SNOMED-CT had overall coverage of 88.7% of the concepts being negated. [Abstract/Link to Full Text]

Nohle DG, Ayers LW
The tissue microarray data exchange specification: a document type definition to validate and enhance XML data.
BMC Med Inform Decis Mak. 2005;5(1):12.
BACKGROUND: The Association for Pathology Informatics (API) Extensible Mark-up Language (XML) TMA Data Exchange Specification (TMA DES) proposed in April 2003 provides a community-based, open source tool for sharing tissue microarray (TMA) data in a common format. Each tissue core within an array has separate data including digital images; therefore an organized, common approach to produce, navigate and publish such data facilitates viewing, sharing and merging TMA data from different laboratories. The AIDS and Cancer Specimen Resource (ACSR) is a HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers HIV-related malignancies and uninfected control tissues in microarrays (TMA) accompanied by de-identified clinical data to approved researchers. Exporting our TMA data into the proposed API specified format offers an opportunity to evaluate the API specification in an applied setting and to explore its usefulness. RESULTS: A document type definition (DTD) that governs the allowed common data elements (CDE) in TMA DES export XML files was written, tested and evolved and is in routine use by the ACSR. This DTD defines TMA DES CDEs which are implemented in an external file that can be supplemented by internal DTD extensions for locally defined TMA data elements (LDE). CONCLUSION: ACSR implementation of the TMA DES demonstrated the utility of the specification and allowed application of a DTD to validate the language of the API specified XML elements and to identify possible enhancements within our TMA data management application. Improvements to the specification have additionally been suggested by our experience in importing other institution's exported TMA data. Enhancements to TMA DES to remove ambiguous situations and clarify the data should be considered. Better specified identifiers and hierarchical relationships will make automatic use of the data possible. Our tool can be used to reorder data and add identifiers; upgrading data for changes in the specification can be automatically accomplished. Using a DTD (optionally reflecting our proposed enhancements) can provide stronger validation of exported TMA data. [Abstract/Link to Full Text]

Holland JL, Wilczynski NL, Haynes RB
Optimal search strategies for identifying sound clinical prediction studies in EMBASE.
BMC Med Inform Decis Mak. 2005;5(1):11.
BACKGROUND: Clinical prediction guides assist clinicians by pointing to specific elements of the patient's clinical presentation that should be considered when forming a diagnosis, prognosis or judgment regarding treatment outcome. The numbers of validated clinical prediction guides are growing in the medical literature, but their retrieval from large biomedical databases remains problematic and this presents a barrier to their uptake in medical practice. We undertook the systematic development of search strategies ("hedges") for retrieval of empirically tested clinical prediction guides from EMBASE. METHODS: An analytic survey was conducted, testing the retrieval performance of search strategies run in EMBASE against the gold standard of hand searching, using a sample of all 27,769 articles identified in 55 journals for the 2000 publishing year. All articles were categorized as original studies, review articles, general papers, or case reports. The original and review articles were then tagged as 'pass' or 'fail' for methodologic rigor in the areas of clinical prediction guides and other clinical topics. Search terms that depicted clinical prediction guides were selected from a pool of index terms and text words gathered in house and through request to clinicians, librarians and professional searchers. A total of 36,232 search strategies composed of single and multiple term phrases were trialed for retrieval of clinical prediction studies. The sensitivity, specificity, precision, and accuracy of search strategies were calculated to identify which were the best. RESULTS: 163 clinical prediction studies were identified, of which 69 (42.3%) passed criteria for scientific merit. A 3-term strategy optimized sensitivity at 91.3% and specificity at 90.2%. Higher sensitivity (97.1%) was reached with a different 3-term strategy, but with a 16% drop in specificity. The best measure of specificity (98.8%) was found in a 2-term strategy, but with a considerable fall in sensitivity to 60.9%. All single term strategies performed less well than 2- and 3-term strategies. CONCLUSION: The retrieval of sound clinical prediction studies from EMBASE is supported by several search strategies. [Abstract/Link to Full Text]

Johnston DJ, Costello SP, Dervan PA, O'Shea DG
Development and preliminary evaluation of the VPS ReplaySuite: a virtual double-headed microscope for pathology.
BMC Med Inform Decis Mak. 2005;5(1):10.
BACKGROUND: Advances in computing and telecommunications have resulted in the availability of a range of online tools for use in pathology training and quality assurance. The majority focus on either enabling pathologists to examine and diagnose cases, or providing image archives that serve as reference material. Limited emphasis has been placed on analysing the diagnostic process used by pathologists to reach a diagnosis and using this as a resource for improving diagnostic performance. METHODS: The ReplaySuite is an online pathology software tool that presents archived virtual slide examinations to pathologists in an accessible video-like format, similar to observing examinations with a double-headed microscope. Delivered through a customized web browser, it utilises PHP (Hypertext PreProcessor) to interact with a remote database and retrieve data describing virtual slide examinations, performed using the Virtual Pathology Slide (VPS). To demonstrate the technology and conduct a preliminary evaluation of pathologists opinions on its potential application in pathology training and quality assurance, 70 pathologists were invited to use the application to review their own and other pathologists examinations of 10 needle-core breast biopsies and complete an electronic survey. 9 pathologists participated, and all subsequently completed an exit survey. RESULTS: Of those who replayed an examination by another pathologist, 83.3% (5/6) agreed that replays provided an insight into the examining pathologists diagnosis and 33.3% (2/6) reconsidered their own diagnosis for at least one case. Of those who reconsidered their original diagnosis, all re-classified either concordant with group consensus or original glass slide diagnosis. 77.7% (7/9) of all participants, and all 3 participants who replayed more than 10 examinations stated the ReplaySuite to be of some or great benefit in pathology training and quality assurance. CONCLUSION: Participants conclude the ReplaySuite to be of some or of great potential benefit to pathology training and quality assurance and consider the ReplaySuite to be beneficial in evaluating the diagnostic trace of an examination. The ReplaySuite removes temporal and spatial issues that surround the use of double-headed microscopes by allowing examinations to be reviewed at different times and in different locations to the original examination. While the evaluation set was limited and potentially subject to bias, the response of participants was favourable. Further work is planned to determine whether use of the ReplaySuite can result in improved diagnostic ability. [Abstract/Link to Full Text]

Bennett NL, Casebeer LL, Kristofco R, Collins BC
Family physicians' information seeking behaviors: a survey comparison with other specialties.
BMC Med Inform Decis Mak. 2005;5(1):9.
BACKGROUND: Using technology to access clinical information has become a critical skill for family physicians. The aims of this study were to assess the way family physicians use the Internet to look for clinical information and how their patterns vary from those of specialists. Further, we sought a better understanding of how family physicians used just-in-time information in clinical practice. METHODS: A fax survey was provided with 17 items. The survey instrument, adapted from two previous studies, was sent to community-based physicians. The questions measured frequency of use and importance of the Internet, palm computers, Internet CME, and email for information seeking and CME. Barriers to use were explored. Demographic data was gathered concerning gender, years since medical school graduation, practice location, practice type, and practice specialty. RESULTS: Family physicians found the Internet to be useful and important as an information source. They were more likely to search for patient oriented material than were specialists who more often searched literature, journals and corresponded with colleagues. Hand held computers were used by almost half of family physicians. CONCLUSION: Family physicians consider the Internet important to the practice of medicine, and the majority use it regularly. Their searches differ from colleagues in other specialties with a focus on direct patient care questions. Almost half of family physicians use hand held computers, most often for drug reference. [Abstract/Link to Full Text]

Haynes RB, Kastner M, Wilczynski NL
Developing optimal search strategies for detecting clinically sound and relevant causation studies in EMBASE.
BMC Med Inform Decis Mak. 2005;5(1):8.
BACKGROUND: Evaluating the existence and strength of an association between a putative cause and adverse clinical outcome is complex and best done by assessing all available evidence. With the increasing burden of chronic disease, greater time demands on health professionals, and the explosion of information, effective retrieval of best evidence has become both more important and more difficult. Optimal search retrieval can be hampered by a number of obstacles, especially poor search strategies, but using empirically tested methodological search filters can enhance the accuracy of searches for sound evidence concerning etiology. Although such filters have previously been developed for studies of relevance to causation in MEDLINE, no empirically tested search strategy exists for EMBASE. METHODS: An analytic survey was conducted, comparing hand searches of journals with retrievals from EMBASE for candidate search terms and combinations. 6 research assistants read all issues of 55 journals indexed in EMBASE. All articles were rated using purpose and quality indicators and categorized into clinically relevant original studies, review articles, general papers, or case reports. The original and review articles were then categorized as 'pass' or 'fail' for scientific merit according to explicit criteria in the areas of causation (etiology) and other clinical topics. Candidate search strategies were developed for causation, then run in a subset of 55 EMBASE journals, the retrievals being compared with the hand search data. The sensitivity, specificity, precision, and accuracy of the search strategies were calculated. RESULTS: Of the 1489 studies classified as causation, 14% were methodologically sound. When search terms were combined, sensitivity reached 92%. Compared with the best single-term strategy, the best combination of terms resulted in an absolute increase in sensitivity (19%) and specificity (5.2%). Maximizing specificity for combined terms resulted in an increase of 7.1% compared with the single term but this came at an expense of sensitivity (39% absolute decrease). A search strategy that optimized the trade-off between sensitivity and specificity achieved 81.9% for sensitivity and 81.4% for specificity. CONCLUSION: We have discovered search strategies that retrieve high quality studies of causation from EMBASE with high sensitivity, high specificity, or an optimal balance of each. [Abstract/Link to Full Text]

Glenton C, Paulsen EJ, Oxman AD
Portals to Wonderland: health portals lead to confusing information about the effects of health care.
BMC Med Inform Decis Mak. 2005 Mar 15;5(1):7.
BACKGROUND: The Internet offers a seemingly endless amount of health information of varying quality. Health portals, which provide entry points to quality-controlled collections of websites, have been hailed as a solution to this problem. The objective of this study is to assess the extent to which government-run health portals provide access to relevant, valid and understandable information about the effects of health care. METHODS: We selected eight clinically relevant questions for which there was a systematic review, searched four portals for answers, and compared the answers we found to the results of the systematic reviews. RESULTS: Our searches resulted in 3400 hits, 155 of which mentioned both the condition and the intervention in one of the eight questions. Sixty-three of the 155 web pages did not give any information about the effect of the intervention. Seventy-seven qualitatively described the effects of the intervention. Twenty-six of these had information that was too unclear to be categorised; 15 were not consistent with the systematic review; and 36 were consistent with the review, but usually did not mention what happens without the intervention, what outcomes have been measured or when they were measured. Fifteen web pages quantitatively described effects. Four of these were abstracts from the systematic review, nine had information that was incomplete and potentially misleading because of a lack of information about people not receiving the intervention and the length of follow-up; one had information that was consistent with the review, but only referred to three trials whereas the review included six; and one was consistent with the review. CONCLUSION: Information accessible through health portals is unlikely to be based on systematic reviews and is often unclear, incomplete and misleading. Portals are only as good as the websites they lead to. Investments in national health portals are unlikely to benefit consumers without investments in the production and maintenance of relevant, valid and understandable information to which the portals lead. [Abstract/Link to Full Text]

Chen D, Orthner HF, Sell SM
Personalized online information search and visualization.
BMC Med Inform Decis Mak. 2005;5(1):6.
BACKGROUND: The rapid growth of online publications such as the Medline and other sources raises the questions how to get the relevant information efficiently. It is important, for a bench scientist, e.g., to monitor related publications constantly. It is also important, for a clinician, e.g., to access the patient records anywhere and anytime. Although time-consuming, this kind of searching procedure is usually similar and simple. Likely, it involves a search engine and a visualization interface. Different words or combination reflects different research topics. The objective of this study is to automate this tedious procedure by recording those words/terms in a database and online sources, and use the information for an automated search and retrieval. The retrieved information will be available anytime and anywhere through a secure web server. RESULTS: We developed such a database that stored searching terms, journals and et al., and implement a piece of software for searching the medical subject heading-indexed sources such as the Medline and other online sources automatically. The returned information were stored locally, as is, on a server and visible through a Web-based interface. The search was performed daily or otherwise scheduled and the users logon to the website anytime without typing any words. The system has potentials to retrieve similarly from non-medical subject heading-indexed literature or a privileged information source such as a clinical information system. The issues such as security, presentation and visualization of the retrieved information were thus addressed. One of the presentation issues such as wireless access was also experimented. A user survey showed that the personalized online searches saved time and increased and relevancy. Handheld devices could also be used to access the stored information but less satisfactory. CONCLUSION: The Web-searching software or similar system has potential to be an efficient tool for both bench scientists and clinicians for their daily information needs. [Abstract/Link to Full Text]

Fontelo P, Liu F, Ackerman M
askMEDLINE: a free-text, natural language query tool for MEDLINE/PubMed.
BMC Med Inform Decis Mak. 2005;5(1):5.
BACKGROUND: Plain language search tools for MEDLINE/PubMed are few. We wanted to develop a search tool that would allow anyone using a free-text, natural language query and without knowing specialized vocabularies that an expert searcher might use, to find relevant citations in MEDLINE/PubMed. This tool would translate a question into an efficient search. RESULTS: The accuracy and relevance of retrieved citations were compared to references cited in BMJ POEMs and CATs (critically appraised topics) questions from the University of Michigan Department of Pediatrics. askMEDLINE correctly matched the cited references 75.8% in POEMs and 89.2 % in CATs questions on first pass. When articles that were deemed to be relevant to the clinical questions were included, the overall efficiency in retrieving journal articles was 96.8% (POEMs) and 96.3% (CATs.) CONCLUSION: askMEDLINE might be a useful search tool for clinicians, researchers, and other information seekers interested in finding current evidence in MEDLINE/PubMed. The text-only format could be convenient for users with wireless handheld devices and those with low-bandwidth connections in remote locations. [Abstract/Link to Full Text]

Brillman JC, Burr T, Forslund D, Joyce E, Picard R, Umland E
Modeling emergency department visit patterns for infectious disease complaints: results and application to disease surveillance.
BMC Med Inform Decis Mak. 2005;5(1):4.
BACKGROUND: Concern over bio-terrorism has led to recognition that traditional public health surveillance for specific conditions is unlikely to provide timely indication of some disease outbreaks, either naturally occurring or induced by a bioweapon. In non-traditional surveillance, the use of health care resources are monitored in "near real" time for the first signs of an outbreak, such as increases in emergency department (ED) visits for respiratory, gastrointestinal or neurological chief complaints (CC). METHODS: We collected ED CCs from 2/1/94 - 5/31/02 as a training set. A first-order model was developed for each of seven CC categories by accounting for long-term, day-of-week, and seasonal effects. We assessed predictive performance on subsequent data from 6/1/02 - 5/31/03, compared CC counts to predictions and confidence limits, and identified anomalies (simulated and real). RESULTS: Each CC category exhibited significant day-of-week differences. For most categories, counts peaked on Monday. There were seasonal cycles in both respiratory and undifferentiated infection complaints and the season-to-season variability in peak date was summarized using a hierarchical model. For example, the average peak date for respiratory complaints was January 22, with a season-to-season standard deviation of 12 days. This season-to-season variation makes it challenging to predict respiratory CCs so we focused our effort and discussion on prediction performance for this difficult category. Total ED visits increased over the study period by 4%, but respiratory complaints decreased by roughly 20%, illustrating that long-term averages in the data set need not reflect future behavior in data subsets. CONCLUSION: We found that ED CCs provided timely indicators for outbreaks. Our approach led to successful identification of a respiratory outbreak one-to-two weeks in advance of reports from the state-wide sentinel flu surveillance and of a reported increase in positive laboratory test results. [Abstract/Link to Full Text]

Eftekhar B, Mohammad K, Ardebili HE, Ghodsi M, Ketabchi E
Comparison of artificial neural network and logistic regression models for prediction of mortality in head trauma based on initial clinical data.
BMC Med Inform Decis Mak. 2005;5(1):3.
BACKGROUND: In recent years, outcome prediction models using artificial neural network and multivariable logistic regression analysis have been developed in many areas of health care research. Both these methods have advantages and disadvantages. In this study we have compared the performance of artificial neural network and multivariable logistic regression models, in prediction of outcomes in head trauma and studied the reproducibility of the findings. METHODS: 1000 Logistic regression and ANN models based on initial clinical data related to the GCS, tracheal intubation status, age, systolic blood pressure, respiratory rate, pulse rate, injury severity score and the outcome of 1271 mainly head injured patients were compared in this study. For each of one thousand pairs of ANN and logistic models, the area under the receiver operating characteristic (ROC) curves, Hosmer-Lemeshow (HL) statistics and accuracy rate were calculated and compared using paired T-tests. RESULTS: ANN significantly outperformed logistic models in both fields of discrimination and calibration but under performed in accuracy. In 77.8% of cases the area under the ROC curves and in 56.4% of cases the HL statistics for the neural network model were superior to that for the logistic model. In 68% of cases the accuracy of the logistic model was superior to the neural network model. CONCLUSIONS: ANN significantly outperformed the logistic models in both fields of discrimination and calibration but lagged behind in accuracy. This study clearly showed that any single comparison between these two models might not reliably represent the true end results. External validation of the designed models, using larger databases with different rates of outcomes is necessary to get an accurate measure of performance outside the development population. [Abstract/Link to Full Text]

Castrén J, Niemi M, Virjo I
Use of email for patient communication in student health care: a cross-sectional study.
BMC Med Inform Decis Mak. 2005 Jan 27;5(1):2.
BACKGROUND: Citizens increasingly use email in personal communication. It is not however clear to what extent physicians utilize it for patient communication. Our study was designed to examine physicians' activity in using email and to estimate the proportion of email messages missing from documentation in electronic patient records (EPR). METHODS: All physicians (n = 76; 48 general practitioners and 28 specialists) at the Finnish Student Health Service received a questionnaire by email, and were asked to print it and keep a daily tally of visits, phone calls and email messages over the study period of one working week (5.5.-9.5.2003). The response rate was 70%. The data originating from the questionnaire were compared with statistical data from the EPR during the study period. RESULTS: The majority (79%, 41/52) of doctors reported using email with patients, averaging 8.6 (range: 0-96) email contacts and a percentage rate of "email / visit" 20% (range: 0-185%) in one working week. Doctors in the capital city region and those doctors who had a positive attitude toward email for patient communication were most active in email use. Up to 73% of email contacts were not documented in the EPR. CONCLUSION: The activity in using email with patients verified among Finnish physicians is compatible with recent study results elsewhere. The notable proportion of un-recorded email messages establishes the need for an electric communication system built into the EPR to improve the quality of patient care and to limit medico-legal risks. [Abstract/Link to Full Text]

Bergman LG, Fors UG
Computer-aided DSM-IV-diagnostics - acceptance, use and perceived usefulness in relation to users' learning styles.
BMC Med Inform Decis Mak. 2005 Jan 7;5(1):1.
BACKGROUND: CDSS (computerized decision support system) for medical diagnostics have been studied for long. This study was undertaken to investigate how different preferences of Learning Styles (LS) of psychiatrists might affect acceptance, use and perceived usefulness of a CDSS for diagnostics in psychiatry. METHODS: 49 psychiatrists (specialists and non-specialists) from 3 different clinics volunteered to participate in this study and to use the CDSS to diagnose a paper-based case (based on a real patient). LS, attitudes to CDSS and complementary data were obtained via questionnaires and interviews. To facilitate the study, a special version of the CDSS was created, which automatically could log interaction details. RESULTS: The LS preferences (according to Kolb) of the 49 physicians turned out as follows: 37% were Assimilating, 31% Converging, 27% Accommodating and 6% Diverging.The CDSS under study seemed to favor psychiatrists with abstract conceptualization information perceiving mode (Assimilating and Converging learning styles).A correlation between learning styles preferences and computer skill was found. Positive attitude to computer-aided diagnostics and learning styles preferences was also found to correlate.Using the CDSS, the specialists produced only 1 correct diagnosis and the non-specialists 2 correct diagnoses (median values) as compared to the three predetermined correct diagnoses of the actual case. Only 10% had all three diagnoses correct, 41 % two correct, 47 % one correct and 2 % had no correct diagnose at all. CONCLUSION: Our results indicate that the use of CDSS does not guarantee correct diagnosis and that LS might influence the results. Future research should focus on the possibility to create systems open to individuals with different LS preferences and possibility to create CDSS adapted to the level of expertise of the user. [Abstract/Link to Full Text]

Backlund L, Skånér Y, Montgomery H, Bring J, Strender LE
GPs' decisions on drug treatment for patients with high cholesterol values: a think-aloud study.
BMC Med Inform Decis Mak. 2004 Dec 13;4(1):23.
BACKGROUND: The purpose was to examine how General Practitioners (GPs) use clinical information and rules from guidelines in their decisions on drug treatment for high cholesterol values. METHODS: Twenty GPs were presented with six case vignettes and were instructed to think aloud while successively more information about a case was presented, and finally to decide if a drug should be prescribed or not. The statements were coded for the clinical information to which they referred and for favouring or not favouring prescription. RESULTS: The evaluation of clinical information was compatible with decision-making as a search for reasons or arguments. Lifestyle-related information like smoking and overweight seemed to be evaluated from different perspectives. A patient's smoking favoured treatment for some GPs and disfavoured treatment for others. CONCLUSIONS: The method promised to be useful for understanding why doctors differ in their decisions on the same patient descriptions and why rules from the guidelines are not followed strictly. [Abstract/Link to Full Text]

Sammouda R, Sammouda M
Modification of the mean-square error principle to double the convergence speed of a special case of Hopfield neural network used to segment pathological liver color images.
BMC Med Inform Decis Mak. 2004 Dec 12;4(1):22.
BACKGROUND: This paper analyzes the effect of the mean-square error principle on the optimization process using a Special Case of Hopfield Neural Network (SCHNN). METHODS: The segmentation of multidimensional medical and colour images can be formulated as an energy function composed of two terms: the sum of squared errors, and a noise term used to avoid the network to be stacked in early local minimum points of the energy landscape. RESULTS: Here, we show that the sum of weighted error, higher than simple squared error, leads the SCHNN classifier to reach faster a local minimum closer to the global minimum with the assurance of acceptable segmentation results. CONCLUSIONS: The proposed segmentation method is used to segment 20 pathological liver colour images, and is shown to be efficient and very effective to be implemented for use in clinics. [Abstract/Link to Full Text]

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Recent Articles in Bulletin of the Medical Library Association

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

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

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

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

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

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

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

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

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

Dudden RF, Coldren S, Condon JE, Katsh S, Reiter CM, Roth PL
Interlibrary loan in primary access libraries: challenging the traditional view.
Bull Med Libr Assoc. 2000 Oct;88(4):303-13.
INTRODUCTION: Primary access libraries serve as the foundation of the National Network of Libraries of Medicine (NN/LM) interlibrary loan (ILL) hierarchy, yet few published reports directly address the important role these libraries play in the ILL system. This may reflect the traditional view that small, primary access libraries are largely users of ILL, rather than important contributors to the effectiveness and efficiency of the national ILL system. OBJECTIVE: This study was undertaken to test several commonly held beliefs regarding ILL system use by primary access libraries. HYPOTHESES: Three hypotheses were developed. HI: Colorado and Wyoming primary access libraries comply with the recommended ILL guideline of adhering to a hierarchical structure, emphasizing local borrowing. H2: The closures of two Colorado Council of Medical Librarians (CCML) primary access libraries in 1996 resulted in twenty-three Colorado primary access libraries' borrowing more from their state resource library in 1997. H3: The number of subscriptions held by Colorado and Wyoming primary access libraries is positively correlated with the number of items they loan and negatively correlated with the number of items they borrow. METHODS: The hypotheses were tested using the 1992 and 1997 DOCLINE and OCLC data of fifty-four health sciences libraries, including fifty primary access libraries, two state resource libraries, and two general academic libraries in Colorado and Wyoming. The ILL data were obtained electronically and analyzed using Microsoft Word 98, Microsoft Excel 98, and JMP 3.2.2. RESULTS: CCML primary access libraries comply with the recommended guideline to emphasize local borrowing by supplying each other with the majority of their ILLs, instead of overburdening libraries located at higher levels in the ILL hierarchy (H1). The closures of two CCML primary access libraries appear to have affected the entire ILL system, resulting in a greater volume of ILL activity for the state resource library and other DOCLINE libraries higher up in the ILL hierarchy and highlighting the contribution made by CCML primary access libraries (H2). CCML primary access libraries borrow and lend in amounts that are proportional to their collection size, rather than overtaxing libraries at higher levels in the ILL hierarchy with large numbers of requests (H3). LIMITATIONS: The main limitations of this study were the small sample size and the use of data collected for another purpose, the CCML ILL survey. CONCLUSIONS: The findings suggest that there is little evidence to support several commonly held beliefs regarding ILL system use by primary access libraries. In addition to validating the important contributions made by primary access libraries to the national ILL system, baseline data that can be used to benchmark current practice performance are provided. [Abstract/Link to Full Text]

Eldredge JD
Evidence-based librarianship: an overview.
Bull Med Libr Assoc. 2000 Oct;88(4):289-302.
OBJECTIVE: To demonstrate how the core characteristics of both evidence-based medicine (EBM) and evidence-based health care (EBHC) can be adapted to health sciences librarianship. METHOD: Narrative review essay involving development of a conceptual framework. The author describes the central features of EBM and EBHC. Following each description of a central feature, the author then suggests ways that this feature applies to health sciences librarianship. RESULTS: First, the decision-making processes of EBM and EBHC are compatible with health sciences librarianship. Second, the EBM and EBHC values of favoring rigorously produced scientific evidence in decision making are congruent with the core values of librarianship. Third, the hierarchical levels of evidence can be applied to librarianship with some modifications. Library researchers currently favor descriptive-survey and case-study methods over systematic reviews, randomized controlled trials, or other higher levels of evidence. The library literature nevertheless contains diverse examples of randomized controlled trials, controlled-comparison studies, and cohort studies conducted by health sciences librarians. CONCLUSIONS: Health sciences librarians are confronted with making many practical decisions. Evidence-based librarianship offers a decision-making framework, which integrates the best available research evidence. By employing this framework and the higher levels of research evidence it promotes, health sciences librarians can lay the foundation for more collaborative and scientific endeavors. [Abstract/Link to Full Text]

Morris RC, Morris DB
J. Michael Homan, Medical Library Association President, 2000-2001.
Bull Med Libr Assoc. 2000 Jul;88(3):275-7. [Abstract/Link to Full Text]

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

Snodgrass GL, Pfeifer MP
The characteristics of medical retraction notices.
Bull Med Libr Assoc. 1992 Oct;80(4):328-34.
During the past twenty years, more than ninety retraction notices have been published in biomedical journals. These retractions constitute a unique body of literature that biomedical researchers, bibliographers, and librarians must monitor to reduce scientific use of retracted, invalid papers. An analysis of medical retraction notices shows that very few are prominent in style, format, or placement, in spite of authoritative publication standards formulated by the International Council of Medical Journal Editors. Although researchers are ultimately responsible for the validity of the information they cite in their own publications, biomedical librarians are in a unique position to educate their patrons regarding retracted papers. [Abstract/Link to Full Text]

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

Press NO
SERHOLD and the public's access to health information.
Bull Med Libr Assoc. 2000 Jul;88(3):269-72. [Abstract/Link to Full Text]

Lipscomb CE
Medical Subject Headings (MeSH).
Bull Med Libr Assoc. 2000 Jul;88(3):265-6. [Abstract/Link to Full Text]

Lewis M
Library requirements and problem-based learning: The Medical Sciences Library, The University of the West Indies.
Bull Med Libr Assoc. 2000 Jul;88(3):255-7. [Abstract/Link to Full Text]

McKnight M
Interlibrary loan availability of nursing journals through DOCLINE and OCLC: a five-state survey.
Bull Med Libr Assoc. 2000 Jul;88(3):254-5. [Abstract/Link to Full Text]

Shisler CM
Positive image and high profile gets results in a hospital library.
Bull Med Libr Assoc. 2000 Jul;88(3):251-3. [Abstract/Link to Full Text]

Rader T, Gagnon AJ
Expediting the transfer of evidence into practice: building clinical partnerships.
Bull Med Libr Assoc. 2000 Jul;88(3):247-50.
A librarian/clinician partnership was fostered in one hospital through the formation of the Evidence-based Practice Committee, with an ulterior goal of facilitating the transfer of evidence into practice. The paper will describe barriers to evidence-based practice and outline the committee's strategies for overcoming these barriers, including the development and promotion of a Web-based guide to evidence-based practice specifically designed for clinicians (health professionals). Educational strategies for use of the Web-based guide will also be addressed. Advantages of this partnership are that the skills of librarians in meeting the needs of clinicians are maximized. The evidence-based practice skills of clinicians are honed and librarians make a valuable contribution to the knowledge-base of the clinical staff. The knowledge acquired through the partnership by both clinicians and librarians will increase the sophistication of the dialogue between the two groups and in turn will expedite the transfer of evidence into practice. [Abstract/Link to Full Text]

Booth A, O'Rourke AJ, Ford NJ
Structuring the pre-search reference interview: a useful technique for handling clinical questions.
Bull Med Libr Assoc. 2000 Jul;88(3):239-46.
OBJECTIVES: To explore whether structuring a literature search request form according to an evidence-based medicine (EBM) anatomy elicits more information, improves precision of search results, and is acceptable to participating librarians. METHODS: Multicenter before-and-after study involved six different libraries. Data from 195 minimally structured forms collected over four months (Phase 1) were compared with data from 185 EBM-structured forms collected over a further four-month period following a brief training intervention (Phase 2). Survey of librarians' attitudes toward using the EBM-structured forms was conducted early during Phase 2. RESULTS: 380 request forms, EBM-structured and minimally structured, were analyzed using SPSS. A statistically significant Pearson correlation was found between use of the EBM-structured form and complexity of the search strategy (P = 0.002). The correlation between clinical requests handled by the EBM-structured form and fewer items retrieved was also statistically significant (P = 0.028). However, librarians rated minimally structured forms more highly than EBM-structured forms against all dimensions except informativeness. CONCLUSIONS: Although use of the EBM-structured forms is associated with more precise searches and more detailed search strategies, considerable work remains on making these forms acceptable to both librarians and users. Nevertheless, with increased familiarity and improved training, information retrieval benefits could be translated into more effective search practice. [Abstract/Link to Full Text]


Standards for vision science libraries. The Association of Vision Science Librarians.
Bull Med Libr Assoc. 2000 Jul;88(3):234-8.
The minimum levels of staffing, services, budget, and technology that should be provided by a library specializing in vision science are presented. The scope and coverage of the collection is described as well. These standards may be used by institutions establishing libraries or by accrediting bodies reviewing existing libraries. [Abstract/Link to Full Text]

Hill DR, Stickell HN
Brandon/Hill selected list of print books and journals in allied health.
Bull Med Libr Assoc. 2000 Jul;88(3):218-33.
This list of 424 books and 77 journals is intended as a selection guide for print literature to be used in a library supporting allied health educational programs or allied health personnel in either an academic or health care setting. Because of the impossibility of covering the large number and wide variety of allied health professions and occupations, the recommended publications are focused primarily on the educational programs listed and recognized by the American Medical Association and other accrediting bodies. Books and journals are categorized by subject; the book list is followed by an author/editor index, and the subject list of journals by an alphabetical title listing. Items suggested for initial purchase (167 books and 31 journals) are indicated by asterisks. To purchase the entire collection of books and journals (2000 subscriptions) would require an expenditure of about $31,970. The cost of only the asterisked items totals $12,515. [Abstract/Link to Full Text]

Garrison JA, Schardt C, Kochi JK
Web-based distance continuing education: a new way of thinking for students and instructors.
Bull Med Libr Assoc. 2000 Jul;88(3):211-7.
As people have more difficulty taking time away from work to attend conferences and workshops, the idea of offering courses via the Web has become more desirable. Addressing a need voiced by Medical Library Association membership, the authors developed a Web-based continuing-education course on the subject of the librarian's role in evidence-based medicine. The aim of the course was to provide medical librarians with a well-constructed, content-rich learning experience available to them at their convenience via the Web. This paper includes a discussion of the considerations that need to be taken into account when developing Web-based courses, the issues that arise when the information delivery changes from face-to-face to online, the changing role of the instructor, and the pros and cons of offering Web-based versus traditional courses. The results of the beta test and future plans for the course are also discussed. [Abstract/Link to Full Text]

Homan JM
T. Scott Plutchak, twenty-third editor of the Bulletin of the Medical Library Association.
Bull Med Libr Assoc. 2000 Apr;88(2):195-6. [Abstract/Link to Full Text]

Bai S, Kelly P
Development of a Web-based faculty publications database.
Bull Med Libr Assoc. 2000 Apr;88(2):189-92. [Abstract/Link to Full Text]

Huber JT, Huggins DW
Assessing electronic information access and use in long-term care facilities in north Texas.
Bull Med Libr Assoc. 2000 Apr;88(2):187-9. [Abstract/Link to Full Text]

Means ML
The Research Funding Service: a model for expanded library services.
Bull Med Libr Assoc. 2000 Apr;88(2):178-86.
Traditionally, libraries have provided a modest amount of information about grants and funding opportunities to researchers in need of research funding. Ten years ago, the University of Washington (UW) Health Sciences Libraries and Information Center joined in a cooperative effort with the School of Medicine to develop a complete, library-based grant and funding service for health sciences researchers called the Research Funding Service. The library provided space, access to the library collection, equipment, and electronic resources, and the School of Medicine funded staff and operations. The range of services now includes individual consultation appointments, an extensive Web site, classes on funding database searching and writing grant applications, a discussion series that frequently hosts guest speakers, a monthly newsletter with funding opportunities of interest to the six health sciences schools, extensive files on funding sources, and referral services. [Abstract/Link to Full Text]

Stevens SR
Mapping the literature of cytotechnology.
Bull Med Libr Assoc. 2000 Apr;88(2):172-7.
The major purpose of this study was to identify and assess indexing coverage of core journals in cytotechnology. It was part of a larger project sponsored by the Nursing and Allied Health Resources Section of the Medical Library Association to map the literature of allied health. Three representative journals in cytotechnology were selected and subjected to citation analysis to determine what journals, other publication types, and years were cited and how often. Bradford's Law of Scattering was applied to the resulting list of cited journals to identify core titles in the discipline, and five indexes were searched to assess coverage of these core titles. Results indicated that the cytotechnology journal literature had a small core but wide dispersion: one third of the 21,021 journal citations appeared in only 3 titles; another third appeared in an additional 26 titles; the remaining third were scattered in 1,069 different titles. Science Citation Index Expanded rated highest in indexing coverage of the core titles, followed by MEDLINE, EMBASE/Excerpta Medica, HealthSTAR, and Cumulative Index to Nursing and Allied Health Literature (CINAHL). The study's results also showed that journals were the predominantly cited format and that citing authors relied strongly on more recent literature. [Abstract/Link to Full Text]

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

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

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

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

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

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

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

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

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

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

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

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Recent Articles in Journal of the American Medical Informatics Association

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

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

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

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

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

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

Sequist TD, Gandhi TK, Karson AS, Fiskio JM, Bugbee D, Sperling M, Cook EF, Orav EJ, Fairchild DG, Bates DW
A randomized trial of electronic clinical reminders to improve quality of care for diabetes and coronary artery disease.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):431-7.
OBJECTIVE: The aim of this study was to evaluate the impact of an integrated patient-specific electronic clinical reminder system on diabetes and coronary artery disease (CAD) care and to assess physician attitudes toward this reminder system. DESIGN: We enrolled 194 primary care physicians caring for 4549 patients with diabetes and 2199 patients with CAD at 20 ambulatory clinics. Clinics were randomized so that physicians received either evidence-based electronic reminders within their patients' electronic medical record or usual care. There were five reminders for diabetes care and four reminders for CAD care. MEASUREMENTS: The primary outcome was receipt of recommended care for diabetes and CAD. We created a summary outcome to assess the odds of increased compliance with overall diabetes care (based on five measures) and overall CAD care (based on four measures). We surveyed physicians to assess attitudes toward the reminder system. RESULTS: Baseline adherence rates to all quality measures were low. While electronic reminders increased the odds of recommended diabetes care (odds ratio [OR] 1.30, 95% confidence interval [CI] 1.01-1.67) and CAD (OR 1.25, 95% CI 1.01-1.55), the impact of individual reminders was variable. A total of three of nine reminders effectively increased rates of recommended care for diabetes or CAD. The majority of physicians (76%) thought that reminders improved quality of care. CONCLUSION: An integrated electronic reminder system resulted in variable improvement in care for diabetes and CAD. These improvements were often limited and quality gaps persist. [Abstract/Link to Full Text]

Sintchenko V, Iredell JR, Gilbert GL, Coiera E
Handheld computer-based decision support reduces patient length of stay and antibiotic prescribing in critical care.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):398-402.
OBJECTIVE: This study assessed the effect of a handheld computer-based decision support system (DSS) on antibiotic use and patient outcomes in a critical care unit. DESIGN: A DSS containing four types of evidence (patient microbiology reports, local antibiotic guidelines, unit-specific antibiotic susceptibility data for common bacterial pathogens, and a clinical pulmonary infection score calculator) was developed and implemented on a handheld computer for use in the intensive care unit at a tertiary referral hospital. System impact was assessed in a prospective "before/after" cohort trial lasting 12 months. Outcome measures were defined daily doses (DDDs) of antibiotics per 1,000 patient-days, patient length of stay, and mortality. RESULTS: The number of admissions, APACHE (Acute Physiology, Age, and Chronic Health Evaluation) II and SAPS (Simplified Acute Physiology Score) II for patients in preintervention, and intervention (DSS use) periods were statistically comparable. The mean patient length of stay and the use of antibiotics in the unit during six months of the DSS use decreased from 7.15 to 6.22 bed-days (p = 0.02) and from 1,767 DDD to 1,458 DDD per 1,000 patient-days (p = 0.04), respectively, with no change in mortality. The DSS was accessed 674 times during 168 days of the trial. Microbiology reports and antibiotic guidelines were the two most commonly used (53% and 22.5%, respectively) types of evidence. The greatest reduction was observed in the use of beta-lactamase-resistant penicillins and vancomycin. CONCLUSION: Handheld computer-based decision support contributed to a significant reduction in patient length of stay and antibiotic prescribing in a critical care unit. [Abstract/Link to Full Text]

Hulse NC, Rocha RA, Del Fiol G, Bradshaw RL, Hanna TP, Roemer LK
KAT: a flexible XML-based knowledge authoring environment.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):418-30.
As part of an enterprise effort to develop new clinical information systems at Intermountain Health Care, the authors have built a knowledge authoring tool that facilitates the development and refinement of medical knowledge content. At present, users of the application can compose order sets and an assortment of other structured clinical knowledge documents based on XML schemas. The flexible nature of the application allows the immediate authoring of new types of documents once an appropriate XML schema and accompanying Web form have been developed and stored in a shared repository. The need for a knowledge acquisition tool stems largely from the desire for medical practitioners to be able to write their own content for use within clinical applications. We hypothesize that medical knowledge content for clinical use can be successfully created and maintained through XML-based document frameworks containing structured and coded knowledge. [Abstract/Link to Full Text]

Wilczynski NL, Haynes RB
Optimal search strategies for detecting clinically sound prognostic studies in EMBASE: an analytic survey.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):481-5.
BACKGROUND: Clinical end users of EMBASE have a difficult time retrieving articles that are both scientifically sound and directly relevant to clinical practice. Search filters have been developed to assist end users in increasing the success of their searches. Many filters have been developed for the literature on therapy and reviews for use in MEDLINE, but little has been done for use in EMBASE with no filter development for studies of prognosis. The objective of this study was to determine how well various methodologic textwords, index terms, and their Boolean combinations retrieve methodologically sound literature on the prognosis of health disorders in EMBASE. METHODS: An analytic survey was conducted, comparing hand searches of 55 journals with retrievals from EMBASE for 4,843 candidate search terms and 8,919 combinations. All articles were rated using purpose and quality indicators, and clinically relevant prognostic articles were categorized as "pass" or "fail" according to explicit criteria for scientific merit. Candidate search strategies were run in EMBASE, the retrievals being compared with the hand search data. The sensitivity, specificity, precision, and accuracy of the search strategies were calculated. RESULTS: Of the 1,064 articles about prognosis, 148 (13.9%) met basic criteria for scientific merit. Combinations of search terms reached peak sensitivities of 98.7% with specificity at 50.6%. Compared with best single terms, best multiple terms increased sensitivity for sound studies by 12.2% (absolute increase), while decreasing specificity (absolute decrease 5.1%) when sensitivity was maximized. Combinations of search terms reached peak specificities of 93.4% with sensitivity at 50.7%. Compared with best single terms, best multiple terms increased specificity for sound studies by 7.1% (absolute increase), while decreasing sensitivity (absolute decrease 8.8%) when specificity was maximized. CONCLUSION: Empirically derived search strategies combining indexing terms and textwords can achieve high sensitivity or specificity for retrieving sound prognostic studies from EMBASE. [Abstract/Link to Full Text]

Melton GB, Hripcsak G
Automated detection of adverse events using natural language processing of discharge summaries.
J Am Med Inform Assoc. 2005 Jul-Aug;12(4):448-57.
OBJECTIVE: To determine whether natural language processing (NLP) can effectively detect adverse events defined in the New York Patient Occurrence Reporting and Tracking System (NYPORTS) using discharge summaries. DESIGN: An adverse event detection system for discharge summaries using the NLP system MedLEE was constructed to identify 45 NYPORTS event types. The system was first applied to a random sample of 1,000 manually reviewed charts. The system then processed all inpatient cases with electronic discharge summaries for two years. All system-identified events were reviewed, and performance was compared with traditional reporting. MEASUREMENTS: System sensitivity, specificity, and predictive value, with manual review serving as the gold standard. RESULTS: The system correctly identified 16 of 65 events in 1,000 charts. Of 57,452 total electronic discharge summaries, the system identified 1,590 events in 1,461 cases, and manual review verified 704 events in 652 cases, resulting in an overall sensitivity of 0.28 (95% confidence interval [CI]: 0.17-0.42), specificity of 0.985 (CI: 0.984-0.986), and positive predictive value of 0.45 (CI: 0.42-0.47) for detecting cases with events and an average specificity of 0.9996 (CI: 0.9996-0.9997) per event type. Traditional event reporting detected 322 events during the period (sensitivity 0.09), of which the system identified 110 as well as 594 additional events missed by traditional methods. CONCLUSION: NLP is an effective technique for detecting a broad range of adverse events in text documents and outperformed traditional and previous automated adverse event detection methods. [Abstract/Link to Full Text]

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

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

Overhage JM
Presentation of the Morris F. Collen Award to Clement J. McDonald, MD.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):241-4. [Abstract/Link to Full Text]

Payne PR, Starren JB
Quantifying visual similarity in clinical iconic graphics.
J Am Med Inform Assoc. 2005 May-Jun;12(3):338-45.
OBJECTIVE: The use of icons and other graphical components in user interfaces has become nearly ubiquitous. The interpretation of such icons is based on the assumption that different users perceive the shapes similarly. At the most basic level, different users must agree on which shapes are similar and which are different. If this similarity can be measured, it may be usable as the basis to design better icons. DESIGN: The purpose of this study was to evaluate a novel method for categorizing the visual similarity of graphical primitives, called Presentation Discovery, in the domain of mammography. Six domain experts were given 50 common textual mammography findings and asked to draw how they would represent those findings graphically. Nondomain experts sorted the resulting graphics into groups based on their visual characteristics. The resulting groups were then analyzed using traditional statistics and hypothesis discovery tools. Strength of agreement was evaluated using computational simulations of sorting behavior. MEASUREMENTS: Sorter agreement was measured at both the individual graphical and concept-group levels using a novel simulation-based method. "Consensus clusters" of graphics were derived using a hierarchical clustering algorithm. RESULTS: The multiple sorters were able to reliably group graphics into similar groups that strongly correlated with underlying domain concepts. Visual inspection of the resulting consensus clusters indicated that graphical primitives that could be informative in the design of icons were present. CONCLUSION: The method described provides a rigorous alternative to intuitive design processes frequently employed in the design of icons and other graphical interface components. [Abstract/Link to Full Text]

Patel VL, Branch T, Cimino A, Norton C, Cimino JJ
Participant perceptions of the influences of the NLM-sponsored Woods Hole medical informatics course.
J Am Med Inform Assoc. 2005 May-Jun;12(3):256-62.
This report provides an evaluation of the National Library of Medicine-sponsored Woods Hole Medical Informatics (WHMI) course and the extent to which the objectives of the program are achieved. Two studies were conducted to examine the participants' perceptions of both the short-term (spring 2002) and the long-term influences (1993 through 2002) on knowledge, skills, and behavior. Data were collected through the use of questionnaires, semistructured telephone interviews, and participant observation methods to provide both quantitative and qualitative assessment. The participants of the spring 2002 course considered the course to be an excellent opportunity to increase their knowledge and understanding of the field of medical informatics as well as to meet and interact with other professionals in the field to establish future collaborations. Past participants remained highly satisfied with their experience at Woods Hole and its influence on their professional careers and their involvement in a broad range of activities related to medical informatics. This group considered their knowledge and understanding of medical informatics to be of greater quality, had increased their networking with other professionals, and were more confident and motivated to work in the field. Many of the participants feel and show evidence of becoming effective agents of change in their institutions in the area of medical informatics, which is one of the objectives of the program. [Abstract/Link to Full Text]

Rothschild AS, Lehmann HP
Information retrieval performance of probabilistically generated, problem-specific computerized provider order entry pick-lists: a pilot study.
J Am Med Inform Assoc. 2005 May-Jun;12(3):322-30.
OBJECTIVE: The aim of this study was to preliminarily determine the feasibility of probabilistically generating problem-specific computerized provider order entry (CPOE) pick-lists from a database of explicitly linked orders and problems from actual clinical cases. DESIGN: In a pilot retrospective validation, physicians reviewed internal medicine cases consisting of the admission history and physical examination and orders placed using CPOE during the first 24 hours after admission. They created coded problem lists and linked orders from individual cases to the problem for which they were most indicated. Problem-specific order pick-lists were generated by including a given order in a pick-list if the probability of linkage of order and problem (PLOP) equaled or exceeded a specified threshold. PLOP for a given linked order-problem pair was computed as its prevalence among the other cases in the experiment with the given problem. The orders that the reviewer linked to a given problem instance served as the reference standard to evaluate its system-generated pick-list. MEASUREMENTS: Recall, precision, and length of the pick-lists. RESULTS: Average recall reached a maximum of .67 with a precision of .17 and pick-list length of 31.22 at a PLOP threshold of 0. Average precision reached a maximum of .73 with a recall of .09 and pick-list length of .42 at a PLOP threshold of .9. Recall varied inversely with precision in classic information retrieval behavior. CONCLUSION: We preliminarily conclude that it is feasible to generate problem-specific CPOE pick-lists probabilistically from a database of explicitly linked orders and problems. Further research is necessary to determine the usefulness of this approach in real-world settings. [Abstract/Link to Full Text]

Sax U, Kohane I, Mandl KD
Wireless technology infrastructures for authentication of patients: PKI that rings.
J Am Med Inform Assoc. 2005 May-Jun;12(3):263-8.
As the public interest in consumer-driven electronic health care applications rises, so do concerns about the privacy and security of these applications. Achieving a balance between providing the necessary security while promoting user acceptance is a major obstacle in large-scale deployment of applications such as personal health records (PHRs). Robust and reliable forms of authentication are needed for PHRs, as the record will often contain sensitive and protected health information, including the patient's own annotations. Since the health care industry per se is unlikely to succeed at single-handedly developing and deploying a large scale, national authentication infrastructure, it makes sense to leverage existing hardware, software, and networks. This report proposes a new model for authentication of users to health care information applications, leveraging wireless mobile devices. Cell phones are widely distributed, have high user acceptance, and offer advanced security protocols. The authors propose harnessing this technology for the strong authentication of individuals by creating a registration authority and an authentication service, and examine the problems and promise of such a system. [Abstract/Link to Full Text]

Staes CJ, Huff SM, Evans RS, Narus SP, Tilley C, Sorensen JB
Development of an information model for storing organ donor data within an electronic medical record.
J Am Med Inform Assoc. 2005 May-Jun;12(3):357-63.
OBJECTIVE: To develop a model to store information in an electronic medical record (EMR) for the management of transplant patients. The model for storing donor information must be designed to allow clinicians to access donor information from the transplant recipient's record and to allow donor data to be stored without needlessly proliferating new Logical Observation Identifier Names and Codes (LOINC) codes for already-coded laboratory tests. DESIGN: Information required to manage transplant patients requires the use of a donor's medical information while caring for the transplant patient. Three strategies were considered: (1) link the transplant patient's EMR to the donor's EMR; (2) use pre-coordinated observation identifiers (i.e., LOINC codes with *(wedge)DONOR specified in the system axes) to identify donor data stored in the transplant patient's EMR; and (3) use an information model that allows donor information to be stored in the transplant patient's record by allowing the "source" of the data (donor) and the "name" of the result (e.g., blood type) to be post-coordinated in the transplant patient's EMR. RESULTS: We selected the third strategy and implemented a flexible post-coordinated information model. There was no need to create new LOINC codes for already-coded laboratory tests. The model required that the data structure in the EMR allow for the storage of the "subject" of the test. CONCLUSION: The selected strategy met our design requirements and provided an extendable information model to store donor data. This model can be used whenever it is necessary to refer to one patient's data from another patient's EMR. [Abstract/Link to Full Text]

Huang Y, Lowe HJ, Klein D, Cucina RJ
Improved identification of noun phrases in clinical radiology reports using a high-performance statistical natural language parser augmented with the UMLS specialist lexicon.
J Am Med Inform Assoc. 2005 May-Jun;12(3):275-85.
OBJECTIVE: The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS(R) Specialist Lexicon to improve noun phrase identification within clinical radiology documents. DESIGN: The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)(R) Clinical Document Architecture (CDA)-compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. RESULTS: The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. CONCLUSION: The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain. [Abstract/Link to Full Text]

Maizlish NA, Herrera L
A record linkage protocol for a diabetes registry at ethnically diverse community health centers.
J Am Med Inform Assoc. 2005 May-Jun;12(3):331-7.
Community health centers serve ethnically diverse populations that may pose challenges for record linkage based on name and date of birth. The objective was to identify an optimal deterministic algorithm to link patient encounters and laboratory results for hemoglobin A1c testing and examine its variability by health center site, patient ethnicity, and other variables. Based on data elements of last name, first name, date of birth, gender, and health center site, matches with >/=50% to < 100% of a maximum score were manually reviewed for true matches. Match keys based on combinations of name substrings, date of birth, gender, and health center were used to link encounter and laboratory files. The optimal match key was the first two letters of the last name and date of birth, which had a sensitivity of 92.7% and a positive predictive value of 99.5%. Sensitivity marginally varied by health center, age, gender, but not by ethnicity. An algorithm that was inexpensive, accurate, and easy to implement was found to be well suited for population-based measurement of clinical quality. [Abstract/Link to Full Text]

Hastings S, Oster S, Langella S, Kurc TM, Pan T, Catalyurek UV, Saltz JH
A grid-based image archival and analysis system.
J Am Med Inform Assoc. 2005 May-Jun;12(3):286-95.
Here the authors present a Grid-aware middleware system, called GridPACS, that enables management and analysis of images in a massive scale, leveraging distributed software components coupled with interconnected computation and storage platforms. The need for this infrastructure is driven by the increasing biomedical role played by complex datasets obtained through a variety of imaging modalities. The GridPACS architecture is designed to support a wide range of biomedical applications encountered in basic and clinical research, which make use of large collections of images. Imaging data yield a wealth of metabolic and anatomic information from macroscopic (e.g., radiology) to microscopic (e.g., digitized slides) scale. Whereas this information can significantly improve understanding of disease pathophysiology as well as the noninvasive diagnosis of disease in patients, the need to process, analyze, and store large amounts of image data presents a great challenge. [Abstract/Link to Full Text]

Winkelman WJ, Leonard KJ, Rossos PG
Patient-perceived usefulness of online electronic medical records: employing grounded theory in the development of information and communication technologies for use by patients living with chronic illness.
J Am Med Inform Assoc. 2005 May-Jun;12(3):306-14.
OBJECTIVE: Patient use of online electronic medical records (EMR) holds the potential to improve health outcomes. The purpose of this study is to discover how patients living with chronic inflammatory bowel disease (IBD) value Internet-based patient access to electronic patient records. DESIGN: This was a qualitative, exploratory, descriptive study using in-depth interviews and focus groups of a total of 12 patients with IBD of at least one-year duration at University Health Network, a tertiary care center in Toronto, Ontario. RESULTS: Four themes have been elucidated that comprise a theoretical framework of patient-perceived information and communication technology usefulness: promotion of a sense of illness ownership, of patient-driven communication, of personalized support, and of mutual trust. CONCLUSIONS: For patients with chronic IBD, simply providing access to electronic medical records has little usefulness on its own. Useful technology for patients with IBD is multifaceted, self-care promoting, and integrated into the patient's already existing health and psychosocial support infrastructure. The four identified themes can serve as focal points for the evaluation of information technology designed for patient use, thus providing a patient-centered framework for developers seeking to adapt existing EMR systems to patient access and use for the purposes of improving health care quality and health outcomes. Further studies in other populations are needed to enhance generalizability of the emergent theory. [Abstract/Link to Full Text]

Porter SC, Kohane IS, Goldmann DA
Parents as partners in obtaining the medication history.
J Am Med Inform Assoc. 2005 May-Jun;12(3):299-305.
OBJECTIVE: Patient-centered information management may overcome barriers that impede high-quality, safe care in the emergency department (ED). The utility of parents' report of medication data via a multimedia, touch screen interface, the asthma kiosk, was investigated. Our specific aims were (1) to estimate the validity of parents' electronically entered medication history for asthma and (2) to compare the parents' kiosk entries regarding medications to the documentation of ED physicians and nurses. METHODS: We enrolled a cohort of parents to use the asthma kiosk and tested the validity of this communication channel for medication data specific to pediatric asthma. Parents' data provided via the kiosk during the ED encounter and the documentation of ED nurses and physicians were compared with a telephone-based interview with the parent after discharge that reviewed all asthma-specific medications physically present in the home. Treating clinicians in the ED were blinded to the parents' kiosk entries. RESULTS: Sixty-six parents were enrolled and 49 of 66 (74.2%) completed the gold standard interview. When analyzed at the level of individual medications, the validity of parental report was 81% for medication name, 79% for route of delivery, 66% for the form of the medication, and 60% for dose. Parents' report improved on the validity of documentation by physicians across all medication details save for medication name. Parents' report was more valid than nursing documentation at triage for all medication details. CONCLUSION: Parents can provide an independent source of medication data that improves on current documentation for key variables that impact quality and safety in emergency asthma care. [Abstract/Link to Full Text]

Westbrook JI, Coiera EW, Gosling AS
Do online information retrieval systems help experienced clinicians answer clinical questions?
J Am Med Inform Assoc. 2005 May-Jun;12(3):315-21.
OBJECTIVE: To assess the impact of clinicians' use of an online information retrieval system on their performance in answering clinical questions. DESIGN: Pre-/post-intervention experimental design. MEASUREMENTS: In a computer laboratory, 75 clinicians (26 hospital-based doctors, 18 family practitioners, and 31 clinical nurse consultants) provided 600 answers to eight clinical scenarios before and after the use of an online information retrieval system. We examined the proportion of correct answers pre- and post-intervention, direction of change in answers, and differences between professional groups. RESULTS: System use resulted in a 21% improvement in clinicians' answers, from 29% (95% confidence interval [CI] 25.4-32.6) correct pre- to 50% (95% CI 46.0-54.0) post-system use. In 33% (95% CI 29.1-36.9) answers were changed from incorrect to correct. In 21% (95% CI 17.1-23.9) correct pre-test answers were supported by evidence found using the system, and in 7% (95% CI 4.9-9.1) correct pre-test answers were changed incorrectly. For 40% (35.4-43.6) of scenarios, incorrect pre-test answers were not rectified following system use. Despite significant differences in professional groups' pre-test scores [family practitioners: 41% (95% CI 33.0-49.0), hospital doctors: 35% (95% CI 28.5-41.2), and clinical nurse consultants: 17% (95% CI 12.3-21.7; chi(2) = 29.0, df = 2, p < 0.01)], there was no difference in post-test scores. (chi(2) = 2.6, df = 2, p = 0.73). CONCLUSIONS: The use of an online information retrieval system was associated with a significant improvement in the quality of answers provided by clinicians to typical clinical problems. In a small proportion of cases, use of the system produced errors. While there was variation in the performance of clinical groups when answering questions unaided, performance did not differ significantly following system use. Online information retrieval systems can be an effective tool in improving the accuracy of clinicians' answers to clinical questions. [Abstract/Link to Full Text]

Giuse NB, Koonce TY, Jerome RN, Cahall M, Sathe NA, Williams A
Evolution of a mature clinical informationist model.
J Am Med Inform Assoc. 2005 May-Jun;12(3):249-55.
Achieving evidence-based practice will require new approaches to providing information during health care delivery and to integrating evidence and informatics at the point of care. To support evidence-based practice, Vanderbilt University Medical Center's Eskind Biomedical Library (EBL) introduced the role of clinical informationist, an information specialist with sufficient knowledge and insight to function as a true partner in the health care team. To further disseminate evidence-based knowledge, the Vanderbilt University Medical Center's (VUMC) electronic medical record system and pathway development processes integrate advanced information synthesis capabilities provided by clinical informationists. Combining clinical informationist expertise with informatics tools is an effective strategy for delivering the evidence needed to support patient care decisions. [Abstract/Link to Full Text]

Galanter WL, Didomenico RJ, Polikaitis A
A trial of automated decision support alerts for contraindicated medications using computerized physician order entry.
J Am Med Inform Assoc. 2005 May-Jun;12(3):269-74.
BACKGROUND: Automated clinical decision support has shown promise in reducing medication errors; however, clinicians often do not comply with alerts. Because renal insufficiency is a common source of medication errors, the authors studied a trial of alerts designed to reduce inpatient administration of medications contraindicated due to renal insufficiency. METHODS: A minimum safe creatinine clearance was established for each inpatient formulary medication. Alerts recommending cancellation appeared when a medication order was initiated for a patient whose estimated creatinine clearance was less than the minimum safe creatinine clearance for the medication. Administration of medications in patients with creatinine clearances less than the medication's minimum safe clearance were studied for 14 months after, and four months before, alert implementation. In addition, the impact of patient age, gender, degree of renal dysfunction, time of day, and duration of housestaff training on the likelihood of housestaff compliance with the alerts was examined. RESULTS: The likelihood of a patient receiving at least one dose of contraindicated drug after the order was initiated decreased from 89% to 47% (p < 0.0001) after alert implementation. Analysis of the alerts seen by housestaff showed that alert compliance was higher in male patients (57% vs. 38%, p = 0.02), increased with the duration of housestaff training (p = 0.04), and increased in patients with worsening renal function (p = 0.007). CONCLUSION: Alerts were effective in decreasing the ordering and administration of drugs contraindicated due to renal insufficiency. Compliance with the alerts was higher in male patients, increased with the duration of housestaff training, and increased in patients with more severe renal dysfunction. [Abstract/Link to Full Text]

Hripcsak G, Rothschild AS
Agreement, the f-measure, and reliability in information retrieval.
J Am Med Inform Assoc. 2005 May-Jun;12(3):296-8.
Information retrieval studies that involve searching the Internet or marking phrases usually lack a well-defined number of negative cases. This prevents the use of traditional interrater reliability metrics like the kappa statistic to assess the quality of expert-generated gold standards. Such studies often quantify system performance as precision, recall, and F-measure, or as agreement. It can be shown that the average F-measure among pairs of experts is numerically identical to the average positive specific agreement among experts and that kappa approaches these measures as the number of negative cases grows large. Positive specific agreement-or the equivalent F-measure-may be an appropriate way to quantify interrater reliability and therefore to assess the reliability of a gold standard in these studies. [Abstract/Link to Full Text]

Wang CJ, Marken RS, Meili RC, Straus JB, Landman AB, Bell DS
Functional characteristics of commercial ambulatory electronic prescribing systems: a field study.
J Am Med Inform Assoc. 2005 May-Jun;12(3):346-56.
OBJECTIVE: To compare the functional capabilities being offered by commercial ambulatory electronic prescribing systems with a set of expert panel recommendations. DESIGN: A descriptive field study of ten commercially available ambulatory electronic prescribing systems, each of which had established a significant market presence. Data were collected from vendors by telephone interview and at sites where the systems were functioning through direct observation of the systems and through personal interviews with prescribers and technical staff. MEASUREMENTS: The capabilities of electronic prescribing systems were compared with 60 expert panel recommendations for capabilities that would improve patient safety, health outcomes, or patients' costs. Each recommended capability was judged as having been implemented fully, partially, or not at all by each system to which the recommendation applied. Vendors' claims about capabilities were compared with the capabilities found in the site visits. RESULTS: On average, the systems fully implemented 50% of the recommended capabilities, with individual systems ranging from 26% to 64% implementation. Only 15% of the recommended capabilities were not implemented by any system. Prescribing systems that were part of electronic health records (EHRs) tended to implement more recommendations. Vendors' claims about their systems' capabilities had a 96% sensitivity and a 72% specificity when site visit findings were considered the gold standard. CONCLUSIONS: The commercial electronic prescribing marketplace may not be selecting for capabilities that would most benefit patients. Electronic prescribing standards should include minimal functional capabilities, and certification of adherence to standards may need to take place where systems are installed and operating. [Abstract/Link to Full Text]

Rood E, Bosman RJ, van der Spoel JI, Taylor P, Zandstra DF
Use of a computerized guideline for glucose regulation in the intensive care unit improved both guideline adherence and glucose regulation.
J Am Med Inform Assoc. 2005 Mar-Apr;12(2):172-80.
OBJECTIVE: To measure the impact of a computerized guideline for glucose regulation in an ICU. DESIGN: A randomized, controlled trial with an off-on-off design. METHODS: We implemented a glucose regulation guideline in an intensive care unit in paper form during the first study period. During the second period, the guideline was randomly applied in either paper or computerized form. In the third period, the guideline was available only in paper form. MEASUREMENTS AND RESULTS: We analyzed data for 484 patients. During the intervention period, the control group included 54 patients and the computerized intervention group included 66 patients. The two guideline-related outcome measures consisted of compliance with: (a) glucose measurement timing recommendations and (b) insulin dose advice. We measured clinical impact as the proportion of time that glucose levels fell within target range. In the first (paper-based) study period, 29.0% of samples occurred with optimal timing; during the second period, this increased to 35.5% for paper-based and to 40.2% for computerized protocols. The third study period timeliness scores reverted to the first period rates. Late (suboptimal) sampling occurred for 66% of glucose measurements in the first study period, for 42% of paper-based and 28% of computer-based protocol samples in the second period, and for 50.0% of samples in the third study period. In the first study period, insulin-dosing guideline compliance was 56.3%; in the second period, it was 64.2% for paper-based and 77.3% for computer-based protocols, and it fell to 42.4% in the third period. For the second study period, the time that a patient's glucose values fell within target range improved for both the control (52.9%) and the computerized groups (54.2%) compared with the first study period (44.3%) and the third period (42.3%). CONCLUSION: Implementing a computerized version of a guideline significantly improved timeliness of measurements and glucose level regulation for critically ill patients compared with implementing a paper-based version of the guideline. [Abstract/Link to Full Text]

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

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

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

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

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

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

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

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Recent Articles in Journal of the Medical Library Association

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

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

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

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

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

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

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

Shultz M
Mapping of medical acronyms and initialisms to Medical Subject Headings (MeSH) across selected systems.
J Med Libr Assoc. 2006 Oct;94(4):410-4.
INTRODUCTION: Given the common use of acronyms and initialisms in the health sciences, searchers may be entering these abbreviated terms rather than full phrases when searching online systems. The purpose of this study is to evaluate how various MEDLINE Medical Subject Headings (MeSH) interfaces map acronyms and initialisms to the MeSH vocabulary. METHODS: The interfaces used in this study were: the PubMed MeSH database, the PubMed Automatic Term Mapping feature, the NLM Gateway Term Finder, and Ovid MEDLINE. Acronyms and initialisms were randomly selected from 2 print sources. The test data set included 415 randomly selected acronyms and initialisms whose related meanings were found to be MeSH terms. Each acronym and initialism was entered into each MEDLINE MeSH interface to determine if it mapped to the corresponding MeSH term. Separately, 46 commonly used acronyms and initialisms were tested. RESULTS: While performance differed widely, the success rates were low across all interfaces for the randomly selected terms. The common acronyms and initialisms tested at higher success rates across the interfaces, but the differences between the interfaces remained. CONCLUSION: Online interfaces do not always map medical acronyms and initialisms to their corresponding MeSH phrases. This may lead to inaccurate results and missed information if acronyms and initialisms are used in search strategies. [Abstract/Link to Full Text]

Tennant MR, Cataldo TT, Sherwill-Navarro P, Jesano R
Evaluation of a liaison librarian program: client and liaison perspectives.
J Med Libr Assoc. 2006 Oct;94(4):402-9, e201-4.
OBJECTIVES: This paper describes a survey-based evaluation of the five-year old Liaison Librarian Program at the University of Florida. METHODS: Liaison librarians, faculty, students, staff, residents, and post-doctoral associates were queried via Web-based surveys. Questions addressed client and liaison perspectives on a variety of issues, including program and service awareness and usage, client-library relations and communication, client support for the program, and liaison workload. RESULTS: Approximately 43% of the 323 client respondents were aware of liaison services; 72% (n = 163) of these clients had had contact with their liaison. Ninety-five percent (n = 101) of faculty and students who reported contact with their liaison supported the continuation of the program. Liaison services were used by a greater percentage of faculty than students, although they had similar patterns of usage and reported the same "traditional" services to be most important. Liaisons indicated that communications with clients had increased, the reputation of the library was enhanced, and their workloads had increased as a result of the Liaison Librarian Program. CONCLUSIONS AND RECOMMENDATIONS: Survey results suggest that the Liaison Librarian Program has a core set of clients who use and highly value the services provided by liaisons. Recommendations addressing workload, training, marketing, and administrative support are provided. [Abstract/Link to Full Text]

Sladek R, Tieman J, Fazekas BS, Abernethy AP, Currow DC
Development of a subject search filter to find information relevant to palliative care in the general medical literature.
J Med Libr Assoc. 2006 Oct;94(4):394-401.
PURPOSE: The research developed and validated palliative care search filters for use in the general biomedical literature. METHODS: Four general medical journals were hand-searched to identify articles relevant to palliative care, forming a "gold standard" reference set. Searches comprising Medical Subject Headings (MeSH) and text-words were created for use in Ovid MEDLINE, and retrieved references were compared to the gold standard. Sensitivity, specificity, accuracy, and precision rates were calculated. RESULTS: By hand-searching 20,501 articles published in the 4 journals during the 3-year study period (1999-2001), reviewers identified 773 items relevant to palliative care (3.8%). A master search combining 9 MeSH descriptors with 3 text-words achieved 45.4% sensitivity, 99.3% specificity, 73% precision, and 97.3% accuracy. Efforts to increase the sensitivity by modifying 3 relevant published but unvalidated searches did not improve the yield, except in 1 case which resulted in an improved sensitivity of 56.9% but was offset by reduced specificity (92.1%), precision (22%), and accuracy (90.8%). CONCLUSIONS: The study confirmed that literature relevant to palliative care is difficult to identify in general medical journals. While the filter developed in this research represents the best trade-off between sensitivity, specificity, accuracy, and precision, the sensitivity is unacceptably low. Further research, such as frequency analysis of text-words and MeSH terms, is required to increase the sensitivity of searching in this subset of the literature. [Abstract/Link to Full Text]

Kaplan R, Steinberg M, Doucette J
Retention of retrospective print journals in the digital age: trends and analysis.
J Med Libr Assoc. 2006 Oct;94(4):387-93, e198-200.
PURPOSE: The issue of retaining retrospective print journals is examined in light of the shift to electronic titles, the reallocation of library budgets from print to electronic, and the changing research practices of today's library users. This article also examines the evolving role of the physical library and its impact on space allocation. METHODS: To determine current practice and opinion, a survey of health sciences librarians and academic librarians was conducted. To demonstrate the use patterns of older journal issues, citation analyses and interlibrary loan statistics were examined. RESULTS: All methods indicate that recent material is accessed more frequently than older material, with a significant drop in use of materials greater than 15 years old. Materials greater than 20 years old constituted less than 5% of interlibrary loans and less than 9% of articles noted in the citation analysis. CONCLUSIONS: It is possible to eliminate older years of a print journal collection without a large impact on the needs of researchers. Librarians' preference to maintain full runs of journal titles may be motivated by reasons outside of actual usage or patrons needs. [Abstract/Link to Full Text]

Patel MR, Schardt CM, Sanders LL, Keitz SA
Randomized trial for answers to clinical questions: evaluating a pre-appraised versus a MEDLINE search protocol.
J Med Libr Assoc. 2006 Oct;94(4):382-7.
OBJECTIVE: The paper compares the speed, validity, and applicability of two different protocols for searching the primary medical literature. DESIGN: A randomized trial involving medicine residents was performed. SETTING: An inpatient general medicine rotation was used. PARTICIPANTS: Thirty-two internal medicine residents were block randomized into four groups of eight. MAIN OUTCOME MEASURES: Success rate of each search protocol was measured by perceived search time, number of questions answered, and proportion of articles that were applicable and valid. RESULTS: Residents randomized to the MEDLINE-first (protocol A) group searched 120 questions, and residents randomized to the MEDLINE-last (protocol B) searched 133 questions. In protocol A, 104 answers (86.7%) and, in protocol B, 117 answers (88%) were found to clinical questions. In protocol A, residents reported that 26 (25.2%) of the answers were obtained quickly or rated as "fast" (<5 minutes) as opposed to 55 (51.9%) in protocol B, (P = 0.0004). A subset of questions and articles (n = 79) were reviewed by faculty who found that both protocols identified similar numbers of answer articles that addressed the questions and were felt to be valid using critical appraisal criteria. CONCLUSION: For resident-generated clinical questions, both protocols produced a similarly high percentage of applicable and valid articles. The MEDLINE-last search protocol was perceived to be faster. However, in the MEDLINE-last protocol, a significant portion of questions (23%) still required searching MEDLINE to find an answer. [Abstract/Link to Full Text]

Jerome RN, Miller RA
Expert synthesis of the literature to support critical care decision making.
J Med Libr Assoc. 2006 Oct;94(4):376-81. [Abstract/Link to Full Text]

Loiselle CG, Lambert SD, Dubois S
Beyond the mere dichotomy of active search versus avoidance of information about the self.
J Med Libr Assoc. 2006 Oct;94(4):375. [Abstract/Link to Full Text]

Case DO, Andrews JE, Johnson JD, Allard SL
Avoiding versus seeking: the relationship of information seeking to avoidance, blunting, coping, dissonance, and related concepts.
J Med Libr Assoc. 2005 Jul;93(3):353-62.
QUESTION: How have theorists and empirical researchers treated the human tendency to avoid discomforting information? DATA SOURCES: A historical review (1890-2004) of theory literature in communication and information studies, coupled with searches of recent studies on uptake of genetic testing and on coping strategies of cancer patients, was performed. STUDY SELECTION: The authors' review of the recent literature included searches of the MEDLINE, PsychInfo, and CINAHL databases between 1992 and summer of 2004 and selective, manual searches of earlier literature. Search strategies included the following subject headings and key words: MeSH headings: Genetic Screening/psychology, Decision Making, Neoplasms/diagnosis/genetics/psychology; CINAHL headings: Genetic Screening, Genetic Counseling, Anxiety, Decision Making, Decision Making/Patient; additional key words: avoidance, worry, monitoring, blunting, cancer. The "Related Articles" function in MEDLINE was used to perform additional "citation pearl" searching. MAIN RESULTS: The assumption that individuals actively seek information underlies much of psychological theory and communication practice, as well as most models of the information-seeking process. However, much research has also noted that sometimes people avoid information, if paying attention to it will cause mental discomfort or dissonance. Cancer information in general and genetic screening for cancer in particular are discussed as examples to illustrate this pattern. CONCLUSION: That some patients avoid knowledge of imminent disease makes avoidance behavior an important area for social and psychological research, particularly with regard to genetic testing. [Abstract/Link to Full Text]

Pagon RA
GeneTests: an online genetic information resource for health care providers.
J Med Libr Assoc. 2006 Jul;94(3):343-8.
OBJECTIVE: This paper describes the GeneTests genetic testing information resource with a focus on the GeneReviews component. METHODS AND FINDINGS: The need for authoritative genetic testing information and issues in the development and maintenance of GeneReviews are discussed: Hampered by lack of currency and content deficits, traditional medical information resources such as textbooks and the published literature are generally inadequate sources of genetic testing information. Problems encountered in developing GeneReviews include the evolution of new authorship models and academic and genetics professionals' skepticism about the quality of Web-based publications. CONCLUSIONS: GeneTests is an authoritative, highly used, and well-regarded resource in the international medical community that is intended for health care providers. Future development issues to address include ways to (1) manage the increasing editing and updating load as content grows and (2) address technical and content issues that need to be considered in displaying GeneReviews as a "just in time" resource in the electronic medical record to achieve the project goal of integrating appropriate use of genetic testing into patient care. [Abstract/Link to Full Text]

Mitchell JA, Fomous C, Fun J
Challenges and strategies of the Genetics Home Reference.
J Med Libr Assoc. 2006 Jul;94(3):336-42.
OBJECTIVE: This paper focuses on the first two years of operation of Genetics Home Reference (GHR), a Web-based resource <http://www.ghr.nlm.nih.gov> for the general public that helps to explain the health implications of findings from the Human Genome Project. METHODS AND FINDINGS: Key challenges of Web-based consumer health communication encountered in the growth and maintenance of GHR are discussed: prioritizing topics for GHR, streamlining the development process while keeping genetic information accurate, and designing a system that helps consumers navigate complex genetic relationships. Various strategies are used to address these challenges. Tying content development to topics of national priority and addressing topics requested by users makes the site increasingly important for both consumers and health professionals. Informatics methods are essential for quality control, particularly for genetic information that changes frequently. Indexing and hierarchical browsing features help to facilitate navigation. CONCLUSIONS: GHR is a credible, dynamic Website that uses lay language to explain the effects of genetic variation on human health. Informatics strategies are key to effective management of a large and expanding body of genetics information. Feedback from formal and informal sources indicates increasing usage and favorable acceptance of GHR. [Abstract/Link to Full Text]

Lyon JA, Tennant MR, Messner KR, Osterbur DL
Carving a niche: establishing bioinformatics collaborations.
J Med Libr Assoc. 2006 Jul;94(3):330-5.
OBJECTIVES: The paper describes collaborations and partnerships developed between library bioinformatics programs and other bioinformatics-related units at four academic institutions. METHODS: A call for information on bioinformatics partnerships was made via email to librarians who have participated in the National Center for Biotechnology Information's Advanced Workshop for Bioinformatics Information Specialists. Librarians from Harvard University, the University of Florida, the University of Minnesota, and Vanderbilt University responded and expressed willingness to contribute information on their institutions, programs, services, and collaborating partners. Similarities and differences in programs and collaborations were identified. RESULTS: The four librarians have developed partnerships with other units on their campuses that can be categorized into the following areas: knowledge management, instruction, and electronic resource support. All primarily support freely accessible electronic resources, while other campus units deal with fee-based ones. These demarcations are apparent in resource provision as well as in subsequent support and instruction. CONCLUSIONS AND RECOMMENDATIONS: Through environmental scanning and networking with colleagues, librarians who provide bioinformatics support can develop fruitful collaborations. Visibility is key to building collaborations, as is broad-based thinking in terms of potential partners. [Abstract/Link to Full Text]

Minie M, Bowers S, Tarczy-Hornoch P, Roberts E, James RA, Rambo N, Fuller S
The University of Washington Health Sciences Library BioCommons: an evolving Northwest biomedical research information support infrastructure.
J Med Libr Assoc. 2006 Jul;94(3):321-9.
SETTING: The University of Washington Health Sciences Libraries and Information Center BioCommons serves the bioinformatics needs of researchers at the university and in the vibrant for-profit and not-for-profit biomedical research sector in the Washington area and region. PROGRAM COMPONENTS: The BioCommons comprises services addressing internal University of Washington, not-for-profit, for-profit, and regional and global clientele. The BioCommons is maintained and administered by the BioResearcher Liaison Team. The BioCommons architecture provides a highly flexible structure for adapting to rapidly changing resources and needs. EVALUATION MECHANISMS: BioCommons uses Web-based pre- and post-course evaluations and periodic user surveys to assess service effectiveness. Recent surveys indicate substantial usage of BioCommons services and a high level of effectiveness and user satisfaction. NEXT STEPS/FUTURE DIRECTIONS: BioCommons is developing novel collaborative Web resources to distribute bioinformatics tools and is experimenting with Web-based competency training in bioinformation resource use. [Abstract/Link to Full Text]

Rein DC
Developing library bioinformatics services in context: the Purdue University Libraries bioinformationist program.
J Med Libr Assoc. 2006 Jul;94(3):314-20, E193-7.
SETTING: Purdue University is a major agricultural, engineering, biomedical, and applied life science research institution with an increasing focus on bioinformatics research that spans multiple disciplines and campus academic units. The Purdue University Libraries (PUL) hired a molecular biosciences specialist to discover, engage, and support bioinformatics needs across the campus. PROGRAM COMPONENTS: After an extended period of information needs assessment and environmental scanning, the specialist developed a week of focused bioinformatics instruction (Bioinformatics Week) to launch system-wide, library-based bioinformatics services. EVALUATION MECHANISMS: The specialist employed a two-tiered approach to assess user information requirements and expectations. The first phase involved careful observation and collection of information needs in-context throughout the campus, attending laboratory meetings, interviewing department chairs and individual researchers, and engaging in strategic planning efforts. Based on the information gathered during the integration phase, several survey instruments were developed to facilitate more critical user assessment and the recovery of quantifiable data prior to planning. NEXT STEPS/FUTURE DIRECTIONS: Given information gathered while working with clients and through formal needs assessments, as well as the success of instructional approaches used in Bioinformatics Week, the specialist is developing bioinformatics support services for the Purdue community. The specialist is also engaged in training PUL faculty librarians in bioinformatics to provide a sustaining culture of library-based bioinformatics support and understanding of Purdue's bioinformatics-related decision and policy making. [Abstract/Link to Full Text]

Chattopadhyay A, Tannery NH, Silverman DA, Bergen P, Epstein BA
Design and implementation of a library-based information service in molecular biology and genetics at the University of Pittsburgh.
J Med Libr Assoc. 2006 Jul;94(3):307-13, E192.
SETTING: In summer 2002, the Health Sciences Library System (HSLS) at the University of Pittsburgh initiated an information service in molecular biology and genetics to assist researchers with identifying and utilizing bioinformatics tools. PROGRAM COMPONENTS: This novel information service comprises hands-on training workshops and consultation on the use of bioinformatics tools. The HSLS also provides an electronic portal and networked access to public and commercial molecular biology databases and software packages. EVALUATION MECHANISMS: Researcher feedback gathered during the first three years of workshops and individual consultation indicate that the information service is meeting user needs. NEXT STEPS/FUTURE DIRECTIONS: The service's workshop offerings will expand to include emerging bioinformatics topics. A frequently asked questions database is also being developed to reuse advice on complex bioinformatics questions. [Abstract/Link to Full Text]

Osterbur DL, Alpi K, Canevari C, Corley PM, Devare M, Gaedeke N, Jacobs DK, Kirlew P, Ohles JA, Vaughan KT, Wang L, Wu Y, Geer RC
Vignettes: Diverse library staff offering diverse bioinformatics services.
J Med Libr Assoc. 2006 Jul;94(3):306, E188-91.
OBJECTIVES: The paper gives examples of the bioinformatics services provided in a variety of different libraries by librarians with a broad range of educational background and training. METHODS: Two investigators sent an email inquiry to attendees of the "National Center for Biotechnology Information's (NCBI) Introduction to Molecular Biology Information Resources" or "NCBI Advanced Workshop for Bioinformatics Information Specialists (NAWBIS)" courses. The thirty-five-item questionnaire addressed areas such as educational background, library setting, types and numbers of users served, and bioinformatics training and support services provided. Answers were compiled into program vignettes. DISCUSSION: The bioinformatics support services addressed in the paper are based in libraries with academic and clinical settings. Services have been established through different means: in collaboration with biology faculty as part of formal courses, through teaching workshops in the library, through one-on-one consultations, and by other methods. Librarians with backgrounds from art history to doctoral degrees in genetics have worked to establish these programs. CONCLUSION: Successful bioinformatics support programs can be established in libraries in a variety of different settings and by staff with a variety of different backgrounds and approaches. [Abstract/Link to Full Text]

Messersmith DJ, Benson DA, Geer RC
A Web-based assessment of bioinformatics end-user support services at US universities.
J Med Libr Assoc. 2006 Jul;94(3):299-305, E156-87.
OBJECTIVES: This study was conducted to gauge the availability of bioinformatics end-user support services at US universities and to identify the providers of those services. The study primarily focused on the availability of short-term workshops that introduce users to molecular biology databases and analysis software. METHODS: Websites of selected US universities were reviewed to determine if bioinformatics educational workshops were offered, and, if so, what organizational units in the universities provided them. RESULTS: Of 239 reviewed universities, 72 (30%) offered bioinformatics educational workshops. These workshops were located at libraries (N = 15), bioinformatics centers (N = 38), or other facilities (N = 35). No such training was noted on the sites of 167 universities (70%). Of the 115 bioinformatics centers identified, two-thirds did not offer workshops. CONCLUSIONS: This analysis of university Websites indicates that a gap may exist in the availability of workshops and related training to assist researchers in the use of bioinformatics resources, representing a potential opportunity for libraries and other facilities to provide training and assistance for this growing user group. [Abstract/Link to Full Text]

Geer RC
Broad issues to consider for library involvement in bioinformatics.
J Med Libr Assoc. 2006 Jul;94(3):286-98, E152-5.
BACKGROUND: The information landscape in biological and medical research has grown far beyond literature to include a wide variety of databases generated by research fields such as molecular biology and genomics. The traditional role of libraries to collect, organize, and provide access to information can expand naturally to encompass these new data domains. METHODS: This paper discusses the current and potential role of libraries in bioinformatics using empirical evidence and experience from eleven years of work in user services at the National Center for Biotechnology Information. FINDINGS: Medical and science libraries over the last decade have begun to establish educational and support programs to address the challenges users face in the effective and efficient use of a plethora of molecular biology databases and retrieval and analysis tools. As more libraries begin to establish a role in this area, the issues they face include assessment of user needs and skills, identification of existing services, development of plans for new services, recruitment and training of specialized staff, and establishment of collaborations with bioinformatics centers at their institutions. CONCLUSIONS: Increasing library involvement in bioinformatics can help address information needs of a broad range of students, researchers, and clinicians and ultimately help realize the power of bioinformatics resources in making new biological discoveries. [Abstract/Link to Full Text]

Kroth PJ, Aspinall EE, Phillips HE
The National Institutes of Health (NIH) Policy on Enhancing Public Access: tracking institutional contribution rates.
J Med Libr Assoc. 2006 Jul;94(3):279-83. [Abstract/Link to Full Text]

Martin ER
Team effectiveness in academic medical libraries: a multiple case study.
J Med Libr Assoc. 2006 Jul;94(3):271-8.
OBJECTIVES: The objective of this study is to apply J. Richard Hackman's framework on team effectiveness to academic medical library settings. METHODS: The study uses a qualitative, multiple case study design, employing interviews and focus groups to examine team effectiveness in three academic medical libraries. Another site was selected as a pilot to validate the research design, field procedures, and methods to be used with the cases. In all, three interviews and twelve focus groups, with approximately seventy-five participants, were conducted at the case study libraries. FINDINGS: Hackman identified five conditions leading to team effectiveness and three outcomes dimensions that defined effectiveness. The participants in this study identified additional characteristics of effectiveness that focused on enhanced communication, leadership personality and behavior, and relationship building. The study also revealed an additional outcome dimension related to the evolution of teams. CONCLUSIONS: Introducing teams into an organization is not a trivial matter. Hackman's model of effectiveness has implications for designing successful library teams. [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]

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

Albert KM
Open access: implications for scholarly publishing and medical libraries.
J Med Libr Assoc. 2006 Jul;94(3):253-62.
PURPOSE: The paper reviews and analyzes the evolution of the open access (OA) publishing movement and its impact on the traditional scholarly publishing model. PROCEDURES: A literature survey and analysis of definitions of OA, problems with the current publishing model, historical developments, funding agency responses, stakeholder viewpoints, and implications for scientific libraries and publishing are performed. FINDINGS: The Internet's transformation of information access has fueled interest in reshaping what many see as a dysfunctional, high-cost system of scholarly publishing. For years, librarians alone advocated for change, until relatively recently when interest in OA and related initiatives spread to the scientific community, governmental groups, funding agencies, publishers, and the general public. CONCLUSIONS: Most stakeholders acknowledge that change in the publishing landscape is inevitable, but heated debate continues over what form this transformation will take. The most frequently discussed remedies for the troubled current system are the "green" road (self-archiving articles published in non-OA journals) and the "gold" road (publishing in OA journals). Both movements will likely intensify, with a multiplicity of models and initiatives coexisting for some time. [Abstract/Link to Full Text]

Robinson JG
Jean Pugh Shipman AHIP, Medical Library Association President 2006-2007.
J Med Libr Assoc. 2006 Jul;94(3):249-52. [Abstract/Link to Full Text]

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

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

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

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

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

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

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

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

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