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1.  AHEC library services: from circuit rider to virtual librarian 
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.
PMCID: PMC35258  PMID: 11055304
2.  The NIF DISCO Framework: Facilitating Automated Integration of Neuroscience Content on the Web 
Neuroinformatics  2010;8(2):10.1007/s12021-010-9068-8.
This paper describes the capabilities of DISCO, an extensible approach that supports integrative Web-based information dissemination. DISCO is a component of the Neuroscience Information Framework (NIF), an NIH Neuroscience Blueprint initiative that facilitates integrated access to diverse neuroscience resources via the Internet. DISCO facilitates the automated maintenance of several distinct capabilities using a collection of files 1) that are maintained locally by the developers of participating neuroscience resources and 2) that are “harvested” on a regular basis by a central DISCO server. This approach allows central NIF capabilities to be updated as each resource’s content changes over time. DISCO currently supports the following capabilities: 1) resource descriptions, 2) “LinkOut” to a resource’s data items from NCBI Entrez resources such as PubMed, 3) Web-based interoperation with a resource, 4) sharing a resource’s lexicon and ontology, 5) sharing a resource’s database schema, and 6) participation by the resource in neuroscience-related RSS news dissemination. The developers of a resource are free to choose which DISCO capabilities their resource will participate in. Although DISCO is used by NIF to facilitate neuroscience data integration, its capabilities have general applicability to other areas of research.
doi:10.1007/s12021-010-9068-8
PMCID: PMC3819210  PMID: 20387131
Data integration; database federation; database interoperation; neuroinformatics
3.  OReFiL: an online resource finder for life sciences 
BMC Bioinformatics  2007;8:287.
Background
Many online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis software. Some have been introduced in special journal issues or websites with a search function, but others remain scattered throughout the Internet and in the published literature. The searchable resources on these sites are collected and maintained manually and are therefore of higher quality than automatically updated sites, but also require more time and effort.
Description
We developed an online resource search system called OReFiL to address these issues. We developed a crawler to gather all of the web pages whose URLs appear in MEDLINE abstracts and full-text papers on the BioMed Central open-access journals. The URLs were extracted using regular expressions and rules based on our heuristic knowledge. We then indexed the online resources to facilitate their retrieval and comparison by researchers. Because every online resource has at least one PubMed ID, we can easily acquire its summary with Medical Subject Headings (MeSH) terms and confirm its credibility through reference to the corresponding PubMed entry. In addition, because OReFiL automatically extracts URLs and updates the index, minimal time and effort is needed to maintain the system.
Conclusion
We developed OReFiL, a search system for online life science resources, which is freely available. The system's distinctive features include the ability to return up-to-date query-relevant online resources introduced in peer-reviewed papers; the ability to search using free words, MeSH terms, or author names; easy verification of each hit following links to the corresponding PubMed entry or to papers citing the URL through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar; and quick confirmation of the existence of an online resource web page.
doi:10.1186/1471-2105-8-287
PMCID: PMC1976328  PMID: 17683589
4.  Effect of Resistance Exercises on Function in Older Adults with Osteoporosis or Osteopenia: A Systematic Review 
Physiotherapy Canada  2012;64(4):386-394.
ABSTRACT
Purpose: To examine the effect of resistance exercises on self-reported physical function and activities of daily living (ADL) in older adults with osteoporosis or osteopenia. Methods: A search of available literature was conducted using PubMed, CINAHL, SPORTDiscus, PEDro, ProQuest Nursing and Allied Health Source, and Cochrane Controlled Trials Register. Studies were included if they involved (1) randomized controlled trials; (2) participants with osteoporosis or osteopenia; (3) resistance exercise as an intervention; and (4) self-report of physical function or ADL. Articles were independently reviewed for quality by two authors using the Physiotherapy Evidence Database (PEDro) scale. Cohen's d effect size was calculated by dividing standardized mean differences by the standard deviation to determine treatment effect in terms of physical function or ADL. Results: Five full-text articles were selected for inclusion. PEDro scores ranged from 5 to 7 (out of 10). Effect size mean differences as a result of resistance intervention ranged from 0.08 to 1.74, suggesting “trivial” to “large” effects on self-reported physical function and ADL. Conclusion: Results suggest that interventions using resistance training have a beneficial impact on the domains of physical function and ADL in participants with osteoporosis or osteopenia. More high-quality studies are needed to lend further validity to this supposition.
doi:10.3138/ptc.2011-31BH
PMCID: PMC3484910  PMID: 23997394
activities of daily living; exercise; osteopenia; osteoporosis; resistance training; activités de la vie quotidienne; exercice; fonction; ostéoporose; ostéopénie; entraînement avec résistance; entraînement en force
5.  Predicting ADL disability in community-dwelling elderly people using physical frailty indicators: a systematic review 
BMC Geriatrics  2011;11:33.
Background
Disability in Activities of Daily Living (ADL) is an adverse outcome of frailty that places a burden on frail elderly people, care providers and the care system. Knowing which physical frailty indicators predict ADL disability is useful in identifying elderly people who might benefit from an intervention that prevents disability or increases functioning in daily life. The objective of this study was to systematically review the literature on the predictive value of physical frailty indicators on ADL disability in community-dwelling elderly people.
Methods
A systematic search was performed in 3 databases (PubMed, CINAHL, EMBASE) from January 1975 until April 2010. Prospective, longitudinal studies that assessed the predictive value of individual physical frailty indicators on ADL disability in community-dwelling elderly people aged 65 years and older were eligible for inclusion. Articles were reviewed by two independent reviewers who also assessed the quality of the included studies.
Results
After initial screening of 3081 titles, 360 abstracts were scrutinized, leaving 64 full text articles for final review. Eventually, 28 studies were included in the review. The methodological quality of these studies was rated by both reviewers on a scale from 0 to 27. All included studies were of high quality with a mean quality score of 22.5 (SD 1.6). Findings indicated that individual physical frailty indicators, such as weight loss, gait speed, grip strength, physical activity, balance, and lower extremity function are predictors of future ADL disability in community-dwelling elderly people.
Conclusions
This review shows that physical frailty indicators can predict ADL disability in community-dwelling elderly people. Slow gait speed and low physical activity/exercise seem to be the most powerful predictors followed by weight loss, lower extremity function, balance, muscle strength, and other indicators. These findings should be interpreted with caution because the data of the different studies could not be pooled due to large variations in operationalization of the indicators and ADL disability across the included studies. Nevertheless, our study suggests that monitoring physical frailty indicators in community-dwelling elderly people might be useful to identify elderly people who could benefit from disability prevention programs.
doi:10.1186/1471-2318-11-33
PMCID: PMC3142492  PMID: 21722355
6.  Functional assessment and performance evaluation for assistive robotic manipulators: Literature review 
Context
The user interface development of assistive robotic manipulators can be traced back to the 1960s. Studies include kinematic designs, cost-efficiency, user experience involvements, and performance evaluation. This paper is to review studies conducted with clinical trials using activities of daily living (ADLs) tasks to evaluate performance categorized using the International Classification of Functioning, Disability, and Health (ICF) frameworks, in order to give the scope of current research and provide suggestions for future studies.
Methods
We conducted a literature search of assistive robotic manipulators from 1970 to 2012 in PubMed, Google Scholar, and University of Pittsburgh Library System – PITTCat.
Results
Twenty relevant studies were identified.
Conclusion
Studies were separated into two broad categories: user task preferences and user-interface performance measurements of commercialized and developing assistive robotic manipulators. The outcome measures and ICF codes associated with the performance evaluations are reported. Suggestions for the future studies include (1) standardized ADL tasks for the quantitative and qualitative evaluation of task efficiency and performance to build comparable measures between research groups, (2) studies relevant to the tasks from user priority lists and ICF codes, and (3) appropriate clinical functional assessment tests with consideration of constraints in assistive robotic manipulator user interfaces. In addition, these outcome measures will help physicians and therapists build standardized tools while prescribing and assessing assistive robotic manipulators.
doi:10.1179/2045772313Y.0000000132
PMCID: PMC3758524  PMID: 23820143
Spinal cord injuries; Paralysis; Robotics; Wheelchairs; Task performance; Assistive technology; Assistive robotic manipulators; User interfaces; Functional assessment; Outcome measures; Disability; Rehabilitation; Physical; Vocational; Activities of daily living; Muscular dystrophy; Spinal cord injury; Spinal muscular atrophy; Multiple sclerosis; Amyotrophic lateral sclerosis; Cerebral palsy; Rheumatoid arthritis; Postpolio syndrome; Locked-in syndrome
7.  Estimated Quality-Adjusted Life-Year Associated with the Degree of Activities of Daily Living in Patients with Alzheimer's Disease 
Background/Aims
The quality-adjusted life-year (QALY) and health state utility values (HSUVs) are major quality of life scales that are used for the analyses of health economics of diseases such as Alzheimer's disease (AD). In Japan, the most common dementia disease is AD with cerebrovascular diseases (CVD), followed by ‘pure’ AD. There is a need to reconsider QALY and HSUVs in the context of activities of daily living (ADL) levels in AD and AD with CVD.
Methods
Studies on QALY and HSUVs based on ADL levels in AD were identified using a PubMed search. HSUVs were estimated in AD patients with ADL levels A (independent walking and eating), B (some problems with walking but sitting without assistance), and C (confined to bed). These three ADL levels correspond approximately to the stages of Mobility on the EQ-5D.
Results
There has been no previous report on HSUVs related to the level of physical activity of patients with AD. From the previous reports and EQ-5D, we estimated that the HSUVs of pure AD and AD with CVD for ADL levels A, B, and C were 0.61 and 0.58, 0.53 and 0.28, and 0.19 and 0.05, respectively.
Conclusion
Effects of ADL should be considered during the decision making process in health policy for dementia care in Japan.
doi:10.1159/000355114
PMCID: PMC3919497  PMID: 24516416
Quality-adjusted life-year; Activities of daily living; Alzheimer's disease

8.  Availability of renal literature in six bibliographic databases 
Clinical Kidney Journal  2012;5(6):610-617.
Background
When searching for renal literature, nephrologists must choose between several different bibliographic databases. We compared the availability of renal clinical studies in six major bibliographic databases.
Methods
We gathered 151 renal systematic reviews, which collectively contained 2195 unique citations referencing primary studies in the form of journal articles, meeting articles or meeting abstracts published between 1963 and 2008. We searched for each citation in three subscription-free bibliographic databases (PubMed, Google Scholar and Scirus) and three subscription-based databases (EMBASE, Ovid-MEDLINE and ISI Web of Knowledge). For the subscription-free databases, we determined which full-text journal articles were available free of charge via links to the article source.
Results
The proportion of journal articles contained within each of the six databases ranged from 96 to 97%; results were similar for meeting articles. Availability of meeting abstracts was poor, ranging from 0 to 37% (P < 0.01) with ISI Web of Knowledge containing the largest proportion [37%, 95% confidence interval (95% CI) 32–43%]. Among the subscription-free databases, free access to full-text articles was highest in Google Scholar (38% free, 95% CI 36–41%), and was only marginally higher (39%) when all subscription-free databases were searched. After 2000, free access to full-text articles increased to 49%.
Conclusions
Over 99% of renal clinical journal articles are available in at least one major bibliographic database. Subscription-free databases provide free full-text access to almost half of the articles published after the year 2000, which may be of particular interest to clinicians in settings with limited access to subscription-based resources.
doi:10.1093/ckj/sfs152
PMCID: PMC3506156  PMID: 23185693
bibliographic databases; content coverage; evidence-based medicine; information storage and retrieval; literature searching; renal informatics
9.  Recognition of activities of daily living in healthy subjects using two ad-hoc classifiers 
Background
Activities of daily living (ADL) are important for quality of life. They are indicators of cognitive health status and their assessment is a measure of independence in everyday living. ADL are difficult to reliably assess using questionnaires due to self-reporting biases. Various sensor-based (wearable, in-home, intrusive) systems have been proposed to successfully recognize and quantify ADL without relying on self-reporting. New classifiers required to classify sensor data are on the rise. We propose two ad-hoc classifiers that are based only on non-intrusive sensor data.
Methods
A wireless sensor system with ten sensor boxes was installed in the home of ten healthy subjects to collect ambient data over a duration of 20 consecutive days. A handheld protocol device and a paper logbook were also provided to the subjects. Eight ADL were selected for recognition. We developed two ad-hoc ADL classifiers, namely the rule based forward chaining inference engine (RBI) classifier and the circadian activity rhythm (CAR) classifier. The RBI classifier finds facts in data and matches them against the rules. The CAR classifier works within a framework to automatically rate routine activities to detect regular repeating patterns of behavior. For comparison, two state-of-the-art [Naïves Bayes (NB), Random Forest (RF)] classifiers have also been used. All classifiers were validated with the collected data sets for classification and recognition of the eight specific ADL.
Results
Out of a total of 1,373 ADL, the RBI classifier correctly determined 1,264, while missing 109 and the CAR determined 1,305 while missing 68 ADL. The RBI and CAR classifier recognized activities with an average sensitivity of 91.27 and 94.36%, respectively, outperforming both RF and NB.
Conclusions
The performance of the classifiers varied significantly and shows that the classifier plays an important role in ADL recognition. Both RBI and CAR classifier performed better than existing state-of-the-art (NB, RF) on all ADL. Of the two ad-hoc classifiers, the CAR classifier was more accurate and is likely to be better suited than the RBI for distinguishing and recognizing complex ADL.
Electronic supplementary material
The online version of this article (doi:10.1186/s12938-015-0050-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s12938-015-0050-4
PMCID: PMC4457983  PMID: 26048452
Naïve Bayes; Random Forest; Activities of daily living; ADL recognition; Wireless sensor; Forward chaining inference engine; Circadian activity rhythm; Rule based inference; Classifiers
10.  Why Do Women Not Use Antenatal Services in Low- and Middle-Income Countries? A Meta-Synthesis of Qualitative Studies 
PLoS Medicine  2013;10(1):e1001373.
In a synthesis of 21 qualitative studies representing the views of more than 1,230 women from 15 countries, Kenneth Finlayson and Soo Downe examine the reasons why many women in low- and middle-income countries do not receive adequate antenatal care.
Background
Almost 50% of women in low- and middle-income countries (LMICs) don't receive adequate antenatal care. Women's views can offer important insights into this problem. Qualitative studies exploring inadequate use of antenatal services have been undertaken in a range of countries, but the findings are not easily transferable. We aimed to inform the development of future antenatal care programmes through a synthesis of findings in all relevant qualitative studies.
Methods and Findings
Using a predetermined search strategy, we identified robust qualitative studies reporting on the views and experiences of women in LMICs who received inadequate antenatal care. We used meta-ethnographic techniques to generate themes and a line-of-argument synthesis. We derived policy-relevant hypotheses from the findings. We included 21 papers representing the views of more than 1,230 women from 15 countries. Three key themes were identified: “pregnancy as socially risky and physiologically healthy”, “resource use and survival in conditions of extreme poverty”, and “not getting it right the first time”. The line-of-argument synthesis describes a dissonance between programme design and cultural contexts that may restrict access and discourage return visits. We hypothesize that centralised, risk-focused antenatal care programmes may be at odds with the resources, beliefs, and experiences of pregnant women who underuse antenatal services.
Conclusions
Our findings suggest that there may be a misalignment between current antenatal care provision and the social and cultural context of some women in LMICs. Antenatal care provision that is theoretically and contextually at odds with local contextual beliefs and experiences is likely to be underused, especially when attendance generates increased personal risks of lost family resources or physical danger during travel, when the promised care is not delivered because of resource constraints, and when women experience covert or overt abuse in care settings.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Although maternal deaths worldwide have almost halved since 1990, according to the latest figures, every day roughly 800 women and adolescent girls still die from the complications of pregnancy or childbirth: in 2010, 287,000 women died during or following pregnancy and childbirth, with almost all of these deaths (99%) occurring in low-resource settings. Most maternal deaths are avoidable, as the interventions to prevent or manage the most common complications (severe bleeding, infections, high blood pressure during pregnancy, and unsafe abortion) are well known. Furthermore, many of these complications can be prevented, detected, or treated during antenatal care visits with trained health workers.
Why Was This Study Done?
The World Health Organization (WHO) recommends a minimum of four antenatal visits per pregnancy, but according to WHO figures, between 2005 and 2010 only 53% of pregnant women worldwide attended the recommended four antenatal visits; in low-income countries, this figure was a disappointing 36%. Unfortunately, despite huge international efforts to promote and provide antenatal care, there has been little improvement in these statistics over the past decade. It is therefore important to investigate the reasons for poor antenatal attendance and to seek the views of users of antenatal care. In this study, the researchers combined studies from low- and middle-income countries (LMICs) that included women's views on antenatal care in a meta-synthesis of qualitative studies (qualitative research uses techniques, such as structured interviews, to gather an in-depth understanding of human behaviour, and a meta-synthesis combines and interprets information across studies, contexts, and populations).
What Did the Researchers Do and Find?
The researchers searched several medical, sociological, and psychological databases to find appropriate qualitative studies published between January 1980 and February 2012 that explored the antenatal care experiences, attitudes, and beliefs of women from LMICs who had chosen to access antenatal care late (after 12 weeks' gestation), infrequently (less than four times), or not at all. The researchers included 21 studies (out of the 2,997 initially identified) in their synthesis, representing the views of 1,239 women from 15 countries (Bangladesh, Benin, Cambodia, Gambia, India, Indonesia, Kenya, Lebanon, Mexico, Mozambique, Nepal, Pakistan, South Africa, Tanzania, and Uganda) who were either interviewed directly or gave their opinion as part of a focus group.
The researchers identified three main themes. The first theme reflects women's views that pregnancy is a healthy state and so saw little reason to visit health professionals when they perceived no risk to their well-being—the researchers called this theme, “pregnancy as socially contingent and physiologically healthy.” The second theme relates to women's limited financial resources, so that even when antenatal care was offered free of charge, the cost of transport to get there, the loss of earnings associated with the visit, and the possibility of having to pay for medicines meant that women were unable to attend—the researchers called this theme “resource use and survival in conditions of extreme poverty.” The third theme the researchers identified related to women's views that the antenatal services were inadequate and that the benefits of attending did not outweigh any potential harms. For example, pregnant women who initially recognized the benefits of antenatal care were often disappointed by the lack of resources they found when they got there and, consequently, decided not to return. The researchers called this theme “not getting it right the first time.”
What Do These Findings Mean?
These findings suggest that there may be a misalignment between the principles that underpin the provision of antenatal care and the beliefs and socio-economic contexts of pregnant women in LMICs, meaning that even high-quality antenatal care may not be used by some pregnant women unless their views and concerns are addressed. The themes identified in this meta-synthesis could provide the basis for a new approach to the design and delivery of antenatal care that takes local beliefs and values and resource availability into account. Such programs might help ensure that antenatal care meets pregnant women's expectations and treats them appropriately so that they want to regularly attend antenatal care.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001373.
Wikipedia describes antenatal care (note that Wikipedia is a free online encyclopedia that anyone can edit)
The World Health Organization has a wealth of information relating to pregnancy, including antenatal care
The UK National Institute for Health and Clinical Excellence has evidence-based guidelines on antenatal care
The White Ribbon Alliance for Safe Motherhood has a series of web pages and links relating to respectful maternity care in LMICs
International Federation of Gynecology and Obstetrics is an international organization with connections to various maternity initiatives in LMICs
International Confederation of Midwives has details of the Millennium Development Goals relating to maternity care
doi:10.1371/journal.pmed.1001373
PMCID: PMC3551970  PMID: 23349622
11.  Drug information resources used by nurse practitioners and collaborating physicians at the point of care in Nova Scotia, Canada: a survey and review of the literature 
BMC Nursing  2006;5:5.
Background
Keeping current with drug therapy information is challenging for health care practitioners. Technologies are often implemented to facilitate access to current and credible drug information sources. In the Canadian province of Nova Scotia, legislation was passed in 2002 to allow nurse practitioners (NPs) to practice collaboratively with physician partners. The purpose of this study was to determine the current utilization patterns of information technologies by these groups of practitioners.
Methods
Nurse practitioners and their collaborating physician partners in Nova Scotia were sent a survey in February 2005 to determine the frequency of use, usefulness, accessibility, credibility, and current/timeliness of personal digital assistant (PDA), computer, and print drug information resources. Two surveys were developed (one for PDA users and one for computer users) and revised based on a literature search, stakeholder consultation, and pilot-testing results. A second distribution to nonresponders occurred two weeks following the first. Data were entered and analysed with SPSS.
Results
Twenty-seven (14 NPs and 13 physicians) of 36 (75%) recipients responded. 22% (6) returned personal digital assistant (PDA) surveys. Respondents reported print, health professionals, and online/electronic resources as the most to least preferred means to access drug information, respectively. 37% and 35% of respondents reported using "both print and electronic but print more than electronic" and "print only", respectively, to search monograph-related drug information queries whereas 4% reported using "PDA only". Analysis of respondent ratings for all resources in the categories print, health professionals and other, and online/electronic resources, indicated that the Compendium of Pharmaceuticals and Specialties and pharmacists ranked highly for frequency of use, usefulness, accessibility, credibility, and current/timeliness by both groups of practitioners. Respondents' preferences and resource ratings were consistent with self-reported methods for conducting drug information queries. Few differences existed between NP and physician rankings of resources.
Conclusion
The use of computers and PDAs remains limited, which is also consistent with preferred and frequent use of print resources. Education for these practitioners regarding available electronic drug information resources may facilitate future computer and PDA use. Further research is needed to determine methods to increase computer and PDA use and whether these technologies affect prescribing and patient outcomes.
doi:10.1186/1472-6955-5-5
PMCID: PMC1590010  PMID: 16822323
12.  A Statewide Approach to Health Care Personnel Maldistribution—The California Area Health Education Center System 
Western Journal of Medicine  1984;140(5):798-802.
An Area Health Education Center (AHEC) system has been established in California to address the maldistribution of physicians and other health care professionals. The AHEC program uses educational incentives to recruit and retain health care personnel in underserved areas by linking the academic resources of university health science centers with local educational and clinical facilities. The medical schools, working in partnership with urban or rural AHECs throughout the state, are implementing educational programs to attract trainees and licensed professionals to work in underserved communities. The California AHEC project entered its fifth year in October of 1983 with the participation of all eight medical schools and the Charles Drew Postgraduate School of Medicine, 35 other health professions schools, 17 independent AHECs and more than 400 clinical training sites. Educational programs are reaching more than 22,000 students and practicing health professionals throughout California. We review the current status of the California AHEC system and use the AHEC programs at Loma Linda University to illustrate the effect this intervention is having.
PMCID: PMC1011113  PMID: 6730500
13.  MedReach: building an Area Health Education Center medical information outreach system for Northwest Ohio*† 
In collaboration with regional partners in northwest Ohio, the Area Health Education Center (AHEC) program at the Medical College of Ohio (MCO) at Toledo is reaching out to underserved areas, helping to provide educational opportunities to health care professionals in these communities. This paper describes the development of MedReach, a medical information outreach system that connects regional AHEC sites to MCO via the Internet. MedReach provides physicians and other health care professionals access and support to search computerized textbooks and databases for current information on medical diagnoses, treatments, and research. A unique aspect of the MedReach project is that users are able to receive personal help with information retrieval by calling or emailing MCO's outreach librarian. Periodically, the AHEC program and the Mulford Library at MCO also sponsor an educational program, titled “Medical Applications of Computers,” for regional practitioners. Current feedback on both the medical information outreach system and the educational program has been positive.
PMCID: PMC116405  PMID: 12113517
14.  BioModels.net Web Services, a free and integrated toolkit for computational modelling software 
Briefings in Bioinformatics  2009;11(3):270-277.
Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of quantitative models in biology. To support this standard, MIRIAM Resources maintains a set of standard data types for annotating models, and provides services for manipulating these annotations. Furthermore, BioModels.net creates controlled vocabularies, such as SBO (Systems Biology Ontology) which strictly indexes, defines and links terms used in Systems Biology. Finally, BioModels Database provides a free, centralised, publicly accessible database for storing, searching and retrieving curated and annotated computational models. Each resource provides a web interface to submit, search, retrieve and display its data. In addition, the BioModels.net team provides a set of Web Services which allows the community to programmatically access the resources. A user is then able to perform remote queries, such as retrieving a model and resolving all its MIRIAM Annotations, as well as getting the details about the associated SBO terms. These web services use established standards. Communications rely on SOAP (Simple Object Access Protocol) messages and the available queries are described in a WSDL (Web Services Description Language) file. Several libraries are provided in order to simplify the development of client software. BioModels.net Web Services make one step further for the researchers to simulate and understand the entirety of a biological system, by allowing them to retrieve biological models in their own tool, combine queries in workflows and efficiently analyse models.
doi:10.1093/bib/bbp056
PMCID: PMC2913671  PMID: 19939940
BioModels.net; Systems Biology; modelling; Web Services; annotation; ontology
15.  Access to electronic health knowledge in five countries in Africa: a descriptive study 
Background
Access to medical literature in developing countries is helped by open access publishing and initiatives to allow free access to subscription only journals. The effectiveness of these initiatives in Africa has not been assessed. This study describes awareness, reported use and factors influencing use of on-line medical literature via free access initiatives.
Methods
Descriptive study in four teaching hospitals in Cameroon, Nigeria, Tanzania and Uganda plus one externally funded research institution in The Gambia. Survey with postgraduate doctors and research scientists to determine Internet access patterns, reported awareness of on-line medical information and free access initiatives; semi structured interviews with a sub-sample of survey participants to explore factors influencing use.
Results
In the four African teaching hospitals, 70% of the 305 postgraduate doctors reported textbooks as their main source of information; 66% had used the Internet for health information in the last week. In two hospitals, Internet cafés were the main Internet access point. For researchers at the externally-funded research institution, electronic resources were their main source, and almost all had used the Internet in the last week. Across all 333 respondents, 90% had heard of PubMed, 78% of BMJ on line, 49% the Cochrane Library, 47% HINARI, and 19% BioMedCentral. HINARI use correlates with accessing the Internet on computers located in institutions. Qualitative data suggested there are difficulties logging into HINARI and that sometimes it is librarians that limit access to passwords.
Conclusion
Text books remain an important resource for postgraduate doctors in training. Internet use is common, but awareness of free-access initiatives is limited. HINARI and other initiatives could be more effective with strong institutional endorsement and management to promote and ensure access.
doi:10.1186/1472-6963-7-72
PMCID: PMC1885254  PMID: 17509132
16.  Teaching Bioinformatics and Neuroinformatics by Using Free Web-based Tools 
CBE Life Sciences Education  2010;9(2):98-107.
This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with anatomy (Mouse Brain Library), quantitative trait locus analysis (WebQTL from GeneNetwork), bioinformatics and gene expression analyses (University of California, Santa Cruz Genome Browser, National Center for Biotechnology Information's Entrez Gene, and the Allen Brain Atlas), and information resources (PubMed). Instructors can use these various websites in concert to teach genetics from the phenotypic level to the molecular level, aspects of neuroanatomy and histology, statistics, quantitative trait locus analysis, and molecular biology (including in situ hybridization and microarray analysis), and to introduce bioinformatic resources. Students use these resources to discover 1) the region(s) of chromosome(s) influencing the phenotypic trait, 2) a list of candidate genes—narrowed by expression data, 3) the in situ pattern of a given gene in the region of interest, 4) the nucleotide sequence of the candidate gene, and 5) articles describing the gene. Teaching materials such as a detailed student/instructor's manual, PowerPoints, sample exams, and links to free Web resources can be found at http://mdcune.psych.ucla.edu/modules/bioinformatics.
doi:10.1187/cbe.09-11-0079
PMCID: PMC2879386  PMID: 20516355
17.  Information-seeking behavior changes in community-based teaching practices*† 
A National Library of Medicine information access grant allowed for a collaborative project to provide computer resources in fourteen clinical practice sites that enabled health care professionals to access medical information via PubMed and the Internet. Health care professionals were taught how to access quality, cost-effective information that was user friendly and would result in improved patient care. Selected sites were located in medically underserved areas and received a computer, a printer, and, during year one, a fax machine. Participants were provided dial-up Internet service or were connected to the affiliated hospital's network. Clinicians were trained in how to search PubMed as a tool for practicing evidence-based medicine and to support clinical decision making. Health care providers were also taught how to find patient-education materials and continuing education programs and how to network with other professionals. Prior to the training, participants completed a questionnaire to assess their computer skills and familiarity with searching the Internet, MEDLINE, and other health-related databases. Responses indicated favorable changes in information-seeking behavior, including an increased frequency in conducting MEDLINE searches and Internet searches for work-related information.
PMCID: PMC442175  PMID: 15243639
18.  GLAD4U: deriving and prioritizing gene lists from PubMed literature 
BMC Genomics  2012;13(Suppl 8):S20.
Background
Answering questions such as "Which genes are related to breast cancer?" usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and creating gene lists. This process is not only time-consuming, but also prone to errors.
Results
We report GLAD4U (Gene List Automatically Derived For You), a new, free web-based gene retrieval and prioritization tool. GLAD4U takes advantage of existing resources of the NCBI to ensure computational efficiency. The quality of gene lists created by GLAD4U for three Gene Ontology (GO) terms and three disease terms was assessed using corresponding "gold standard" lists curated in public databases. For all queries, GLAD4U gene lists showed very high recall but low precision, leading to low F-measure. As a comparison, EBIMed's recall was consistently lower than GLAD4U, but its precision was higher. To present the most relevant genes at the top of a list, we studied two prioritization methods based on publication count and the hypergeometric test, and compared the ranked lists and those generated by EBIMed to the gold standards. Both GLAD4U methods outperformed EBIMed for all queries based on a variety of quality metrics. Moreover, the hypergeometric method allowed for a better performance by thresholding genes with low scores. In addition, manual examination suggests that many false-positives could be explained by the incompleteness of the gold standards. The GLAD4U user interface accepts any valid queries for PubMed, and its output page displays the ranked gene list and information associated with each gene, chronologically-ordered supporting publications, along with a summary of the run and links for file export and functional enrichment and protein interaction network analysis.
Conclusions
GLAD4U has a high overall recall. Although precision is generally low, the prioritization methods successfully rank truly relevant genes at the top of the lists to facilitate efficient browsing. GLAD4U is simple to use, and its interface can be found at: http://bioinfo.vanderbilt.edu/glad4u.
doi:10.1186/1471-2164-13-S8-S20
PMCID: PMC3535723  PMID: 23282288
19.  Clinician Search Behaviors May Be Influenced by Search Engine Design 
Background
Searching the Web for documents using information retrieval systems plays an important part in clinicians’ practice of evidence-based medicine. While much research focuses on the design of methods to retrieve documents, there has been little examination of the way different search engine capabilities influence clinician search behaviors.
Objectives
Previous studies have shown that use of task-based search engines allows for faster searches with no loss of decision accuracy compared with resource-based engines. We hypothesized that changes in search behaviors may explain these differences.
Methods
In all, 75 clinicians (44 doctors and 31 clinical nurse consultants) were randomized to use either a resource-based or a task-based version of a clinical information retrieval system to answer questions about 8 clinical scenarios in a controlled setting in a university computer laboratory. Clinicians using the resource-based system could select 1 of 6 resources, such as PubMed; clinicians using the task-based system could select 1 of 6 clinical tasks, such as diagnosis. Clinicians in both systems could reformulate search queries. System logs unobtrusively capturing clinicians’ interactions with the systems were coded and analyzed for clinicians’ search actions and query reformulation strategies.
Results
The most frequent search action of clinicians using the resource-based system was to explore a new resource with the same query, that is, these clinicians exhibited a “breadth-first” search behaviour. Of 1398 search actions, clinicians using the resource-based system conducted 401 (28.7%, 95% confidence interval [CI] 26.37-31.11) in this way. In contrast, the majority of clinicians using the task-based system exhibited a “depth-first” search behavior in which they reformulated query keywords while keeping to the same task profiles. Of 585 search actions conducted by clinicians using the task-based system, 379 (64.8%, 95% CI 60.83-68.55) were conducted in this way.
Conclusions
This study provides evidence that different search engine designs are associated with different user search behaviors.
doi:10.2196/jmir.1396
PMCID: PMC2956236  PMID: 20601351
Clinician; search behavior; information retrieval; Internet
20.  The Cost and Impact of Scaling Up Pre-exposure Prophylaxis for HIV Prevention: A Systematic Review of Cost-Effectiveness Modelling Studies 
PLoS Medicine  2013;10(3):e1001401.
Gabriela Gomez and colleagues systematically review cost-effectiveness modeling studies of pre-exposure prophylaxis (PrEP) for preventing HIV transmission and identify the main considerations to address when considering the introduction of PrEP to HIV prevention programs.
Background
Cost-effectiveness studies inform resource allocation, strategy, and policy development. However, due to their complexity, dependence on assumptions made, and inherent uncertainty, synthesising, and generalising the results can be difficult. We assess cost-effectiveness models evaluating expected health gains and costs of HIV pre-exposure prophylaxis (PrEP) interventions.
Methods and Findings
We conducted a systematic review comparing epidemiological and economic assumptions of cost-effectiveness studies using various modelling approaches. The following databases were searched (until January 2013): PubMed/Medline, ISI Web of Knowledge, Centre for Reviews and Dissemination databases, EconLIT, and region-specific databases. We included modelling studies reporting both cost and expected impact of a PrEP roll-out. We explored five issues: prioritisation strategies, adherence, behaviour change, toxicity, and resistance. Of 961 studies retrieved, 13 were included. Studies modelled populations (heterosexual couples, men who have sex with men, people who inject drugs) in generalised and concentrated epidemics from Southern Africa (including South Africa), Ukraine, USA, and Peru. PrEP was found to have the potential to be a cost-effective addition to HIV prevention programmes in specific settings. The extent of the impact of PrEP depended upon assumptions made concerning cost, epidemic context, programme coverage, prioritisation strategies, and individual-level adherence. Delivery of PrEP to key populations at highest risk of HIV exposure appears the most cost-effective strategy. Limitations of this review include the partial geographical coverage, our inability to perform a meta-analysis, and the paucity of information available exploring trade-offs between early treatment and PrEP.
Conclusions
Our review identifies the main considerations to address in assessing cost-effectiveness analyses of a PrEP intervention—cost, epidemic context, individual adherence level, PrEP programme coverage, and prioritisation strategy. Cost-effectiveness studies indicating where resources can be applied for greatest impact are essential to guide resource allocation decisions; however, the results of such analyses must be considered within the context of the underlying assumptions made.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Every year approximately 2.5 million people are infected with HIV, the virus that causes AIDS. Behavioral strategies like condom use and reduction of sexual partners have been the hallmarks of HIV prevention efforts. However, biological prevention measures have also recently been shown to be effective. These include male circumcision, treatment as prevention (treating HIV-infected people with antiretroviral drugs to reduce transmission), and pre-exposure prophylaxis (PrEP), where people not infected with HIV take antiretroviral drugs to reduce the probability of transmission. Strategies such as PrEP may be viable prevention measure for couples in long-term relationships where one partner is HIV-positive and the other is HIV-negative (HIV serodiscordant couples) or groups at higher risk of HIV infection, such as men who have sex with men, and injection drug users.
Why Was This Study Done?
The findings from recent clinical trials that demonstrate PrEP can reduce HIV transmission have led to important policy discussions and in the US, Southern Africa, and the UK new clinical guidelines have been developed on the use of PrEP for the prevention of HIV infection. For those countries that are considering whether to introduce PrEP into HIV prevention programs, national policy and decision makers need to determine potential costs and health outcomes. Cost-effectiveness models—mathematical models that simulate cost and health effects of different interventions—can help inform such decisions. However, the cost-effectiveness estimates that could provide guidance for PrEP programs are dependent on, and limited by, the assumptions included in the models, which can make their findings difficult to generalize. A systematic comparison of published cost-effectiveness models of HIV PrEP interventions would be useful for policy makers who are considering introducing PrEP intervention programs.
What Did the Researchers Do and Find?
The researchers performed a systematic review to identify published cost-effectiveness models that evaluated the health gains and costs of HIV PrEP interventions. Systematic reviews attempt to identify, appraise, and synthesize all the empirical evidence that meets pre-specified eligibility criteria to answer a given research question by using explicit methods aimed at minimizing bias. By searching databases the authors identified 13 published studies that evaluated the impact of PrEP in different populations (heterosexual couples, men who have sex with men, and injection drug users) in different geographic settings, which included Southern Africa, Ukraine, US, and Peru.
The authors identified seven studies that assessed the introduction of PrEP into generalized HIV epidemics in Southern Africa. These studies suggest that PrEP may be a cost effective intervention to prevent heterosexual transmission. However, the authors note that funding PrEP while other cost-effective HIV prevention methods are underfunded in this setting may have high opportunity costs. The authors identified five studies where PrEP was introduced for concentrated epidemics among men who have sex with men (four studies in the US and one in Peru). These studies suggest that PrEP may have a substantial impact on the HIV epidemic but may not be affordable at current drug prices. The authors also identified a single study that modeled the introduction of PrEP for people who inject drugs in the Ukraine, which found PrEP not to be cost effective.
In all settings the price of antiretroviral drugs was found to be a limiting factor in terms of affordability of PrEP programs. Behavioral changes and adherence to PrEP were estimated to have potentially significant impacts on program effectiveness but the emergence of drug resistance or PrEP-related toxicity did not significantly affect cost-effectiveness estimates. Several PrEP prioritization strategies were explored in included studies and delivering PrEP to populations at highest risk of HIV exposure was shown to improve cost-effectiveness estimates. However, the extra costs of identifying and engaging with high-risk populations were not taken into consideration. The authors note that the geographic coverage of identified studies was limited and that the findings are very dependent on the setting which limits generalizability.
What Do these Findings Mean?
These findings suggest that PrEP could be a cost-effective tool to reduce new HIV infections in some settings. However, the cost-effectiveness of PrEP is dependent upon cost, the epidemic context, program coverage and prioritization strategies, participants' adherence to the drug regimen, and PrEP efficacy estimates. These findings will aid decision makers quantify and compare the reductions in HIV incidence that could be achieved by implementing a PrEP program.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001401.
The US National Institute of Allergy and Infectious Diseases has information on HIV/AIDS
aidsmap provides basic information about HIV/AIDS, summaries of recent research findings on HIV care and treatment, and has a section on PrEP
Information is available from Avert, an international AIDS charity, on many aspects of HIV/AIDS, including HIV prevention
AVAC Global Advocacy for HIV Prevention provides information on HIV prevention, including PrEP
The US Centers for Disease Control and Prevention also has information on PrEP
The World Health Organization has a page on its WHO-CHOICE criteria for cost-effectiveness
doi:10.1371/journal.pmed.1001401
PMCID: PMC3595225  PMID: 23554579
21.  Electronic Biomedical Literature Search for Budding Researcher 
Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature, levels of evidence, and detail about features of search engine as available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research.
doi:10.7860/JCDR/2013/6348.3399
PMCID: PMC3809676  PMID: 24179937
Research; Steps in literature search; Search engine; Literature review; Level of evidence
22.  PHL5/412: On-line Medication Information for Patients: The Pharmacy Infobutton 
Introduction
Several strategies and techniques have been explored for providing health care professionals with automated access to information resources. Insufficient evidence is available though as to how this issue should be approached from the side of patients. Problems already identified in this respect are the verification of information quality and the navigation to appropriate sources. The "infobutton" application developed at Columbia University attempts to provide a comprehensive solution to both. In this paper we present the strategy employed in the development of a pharmacy infobutton offering patients "one touch access" to medication-related information available on public web sites.
Methods
The development of an information button involves four consecutive phases. 1) Identifying the users' questions Users' likely questions were elicited from several complementary sources: a) publications regarding information demands on traditional drug information resources b) users' questions submitted to web sites covering the topic of medications c) information gaps as they are offset by the commonest medication misuses d) recommendations of regulatory authorities for the provision of medication information to the public. Subsequently we used the identified topics to construct generic question templates which are utilised in query formulation. 2) Identifying the appropriate information source Sites were identified and reviewed with respect to quality of content, using predefined evaluation checklists. Consequently a database was created containing URLs of pertinent HTML documents and indexing information. 3) Composing a retrieval strategy. All medications prescribed at Columbia-Presbyterian are represented in coded form in the Medical Entities Dictionary (MED). Queries to the URL database can be constructed using trade/generic names or ingredient terms taken from the MED, in combination with generic question templates. 4) Presenting the results to the user. The Patient Clinical Information System (PatCIS) places an infobutton icon next to each drug name. When users select an infobutton they are presented with a list of possible questions of interest. Each question is a link to one or more resources, using medication-specific queries.
Results
Information buttons linked to Medline and Micromedex are presently available for all medications in the MED. Those providing access to Internet resources will be offered for a restricted number of medications, in an initial pilot phase. Recruitment of patients is under way for a first round of identifying the application's usefulness and shortcomings.
Discussion
The role of the Internet in the process of health care delivery continues to grow, increasing the demand for applications that make efficient use of the medium's capabilities. The PatCIS "infobuttons" are such an application offering an innovative approach to the challenge of enhancing public awareness of health issues.
doi:10.2196/jmir.1.suppl1.e86
PMCID: PMC1761728
Internet; Drug Information Services; Patient Education; Clinical Pharmacy Information Systems
23.  Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization 
PLoS ONE  2013;8(4):e55814.
Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons – Attribution – Share Alike (CC BY-SA) license.
doi:10.1371/journal.pone.0055814
PMCID: PMC3629104  PMID: 23613707
24.  Limitation of activities of daily living accompanying reduced neck mobility after laminoplasty preserving or reattaching the semispinalis cervicis into axis 
European Spine Journal  2007;17(3):415-420.
Although difficulties with neck mobility often interfere with patients’ activities of daily living (ADL) after cervical laminoplasty, there was no detailed study on the relation between the limitations of ADL accompanying postoperative reduced neck mobility and the cervical posterior approach. The aim of this study was to compare retrospectively the frequency of limitations of ADL accompanying neck mobility after laminoplasty preserving the semispinalis cervicis inserted into the C2 spinous process with that after laminoplasty reattaching the muscle to C2. Forty-nine patients after C4–C7 laminoplasty with C3 laminectomy preserving the semispinalis cervicis inserted into C2 (Group A) and 24 patients after C3–C7 laminoplasty reattaching the muscle (Group B) were evaluated. The frequency of postoperative limitations of ADL accompanying each of three neck movements of extension, flexion and rotation were investigated. The postoperative O–C7 angles at extension and flexion was measured on lateral extension and flexion radiographs of the cervical spine, respectively. The postoperative cervical range of motion in rotation was measured in the cranial view using a digital camera. Frequency of limitations of ADL accompanying extension was lower (P = 0.037) in Group A (2%) than in Group B (17%). Frequency of limitations of ADL accompanying flexion was similar in Group A (8%) and Group B (4%). Frequency of limitations of ADL accompanying rotation was lower (P = 0.031) in Group A (12%) than in Group B (33%). Average O–C7 angle at extension was significantly larger (P = 0.002) in Group A (147°) than in Group B (136°). Average O–C7 angle at flexion was similar in Group A (93°) and Group B (91°). Average range of motion in rotation was significantly larger (P = 0.004) in Group A (110°) than in Group B (91°). This retrospective study suggested that the frequency of limitations of ADL accompanying neck extension or rotation was lower after laminoplasty preserving the semispinalis cervicis inserted into C2 than after laminoplasty reattaching the muscle.
doi:10.1007/s00586-007-0553-1
PMCID: PMC2270385  PMID: 18038160
Cervical laminoplasty; Activities of daily living (ADL); Cervical myelopathy; Semispinalis cervicis muscle; Surgical outcome
25.  Interactive query workstation: a demonstration of the practical use of UMLS knowledge sources. 
The Interactive Query Workstation (IQW) has been developed to provide clinicians with a uniform program interface for retrieving medical-related information from various computer-based information resources. These resources can vary in content (bibliographic databases, drug information, general medical text databases), function (article retrieval, differential diagnosis, drug interaction detection, or drug dosage and administration information), and media formats (local hard disk, CD-ROM, local area network, or distant telecommunication link). IQW allows modular addition of new resources as well as extension of previously installed resources. The National Library of Medicine's three Unified Medical Language System (UMLS) Knowledge Sources, the Metathesaurus (Meta), the Semantic Network, and the Information Sources Map (ISM) have been incorporated into many aspects of IQW. Meta provides information about medical terminology and aids IQW in isolating the basic concepts from a clinician's question. The Semantic Network provides information about the categorization of concepts and possible relations between concepts. It also assists IQW in determining which queries are appropriate for a set of concepts contained in the clinician's question. The ISM provides information about the content available from a computer-based resources and aids IQW in selecting an appropriate resource from which to collect information. The computer-based resource selection is performed without user intervention. This interactive demonstration shows an environment which increases the accessibility of medical information to clinicians by utilizing the three UMLS Knowledge Sources.
PMCID: PMC2247999  PMID: 1483001

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