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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.  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
5.  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
6.  Population Impact of Arthritis on Disability in Older Adults 
Arthritis and rheumatism  2006;55(2):248-255.
Objective
Disability threatens the independence of older adults and has large economic and societal costs. This article examines the population impact of arthritis on disability incidence among older Americans.
Methods
The present study used longitudinal data (1998–2000) from the Health and Retirement Study, a national probability sample of elderly Americans. Disability was defined by the inability to perform basic activities of daily living (ADL). A total of 7,758 participants ages ≥65 years with no ADL disability at baseline were included in the analyses. Multiple logistic regression was used to measure the impact of baseline arthritis (self reported) on incidence of subsequent ADL disability after controlling for baseline differences in demographics, health factors, health behaviors, and medical access.
Results
Older adults who had baseline arthritis had a substantially higher incidence of ADL disability compared with those without arthritis (9.3% versus 4.5%). The strong relationship of arthritis and ADL disability was partially explained by demographic, health, behavioral, and medical access factors. However, even after adjusting for all other risk factors, arthritis remained as an independent and significant predictor for developing ADL disability (adjusted odds ratio 1.5, 95% confidence interval 1.2–1.8). Almost 1 in every 4 new cases of ADL disability was due to arthritis (adjusted population attributable fraction: 23.7%).
Conclusion
The high frequency of incident ADL disability attributable to arthritis points to the importance of intervention programs that address the entire spectrum of health and functional problems in persons with arthritis to prevent disability.
doi:10.1002/art.21842
PMCID: PMC2757646  PMID: 16583415
Arthritis; ADL; Longitudinal data; Disability
7.  Measuring Prognosis and Case Mix in Hospitalized Elders 
OBJECTIVE
Although physical function is believed to be an important predictor of outcomes in older people, it has seldom been used to adjust for prognosis or case mix in evaluating mortality rates or resource use. The goal of this study was to determine whether patients’ activity of daily living (ADL) function on admission provided information useful in adjusting for prognosis and case mix after accounting for routine physiologic measures and comorbid diagnoses.
SETTING
The general medical service of a teaching hospital.
PARTICIPANTS
Medical inpatients (n = 823) over age 70 (mean age 80.7, 68% women).
MEASUREMENTS
Independence in ADL function on admission was assessed by interviewing each patient’s primary nurse. We determined the APACHE II Acute Physiology Score (APS) and the Charlson comorbidity score from chart review. Outcome measures were hospital and 1-year mortality, nursing home use in the 90 days following discharge, and cost of hospitalization. Patients were divided into four quartiles according to the number of ADLs in which they were dependent.
MAIN RESULTS
ADL category stratified patients into groups that were at markedly different risks of mortality and higher resource use. For example, hospital mortality varied from 0.9% in patients dependent in no ADL on admission, to 17.4% in patients dependent in all ADLs. One-year mortality ranged from 17.5% to 54.9%, nursing home use from 3% to 33%, and hospital costs varied by 53%. In multivariate analyses controlling for APS, Charlson scores, and demographic characteristics, compared with patients dependent in no ADL, patients dependent in all ADLs were at greater risk of hospital mortality (odds ratio [OR] 13.7; 95% confidence interval [CI] 3.1–58.8), 1-year mortality (OR 4.4; 2.7–7.4), and 90-day nursing home use (OR 14.9; 6.0–37.0). The DRG-adjusted hospital cost was 50% higher for patients dependent in all ADLs. ADL function also improved the discrimination of hospital and 1-year mortality models that considered APS, or Charlson scores, or both.
CONCLUSIONS
ADL function contains important information about prognosis and case mix beyond that provided by routine physiologic data and comorbidities in hospitalized elders. Prognostic and case–mix adjustment methods may be improved if they include measures of function, as well as routine physiologic measures and comorbidity.
doi:10.1046/j.1525-1497.1997.012004203.x
PMCID: PMC1497092  PMID: 9127223
prognosis; case mix; activities of daily living; severity; functional status
8.  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
9.  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
10.  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
11.  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
12.  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
13.  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
14.  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
15.  Outcomes research resources in India: current status, need and way forward 
SpringerPlus  2013;2:518.
Background
Despite their importance, the number of outcomes research studies conducted in India are lesser than other countries. Information about the distribution of existing outcomes research resources and relevant expertise can benefit researchers and research groups interested in conducting outcomes research studies and policy makers interested in funding outcomes research studies in India. We have reviewed the literature to identify and map resources described in outcomes research studies conducted in India.
Methods
We reviewed the following online biomedical databases: Pubmed, SCIRUS, CINAHL, and Google scholar and selected articles that met the following criteria: published in English, conducted on Indian population, providing information about outcomes research resources (databases/registries/electronic medical records/electronic healthcare records/hospital information systems) in India and articles describing outcomes research studies or epidemiological studies based on outcomes research resources. After shortlisting articles, we abstracted data into three datasets viz. 1. Resource dataset, 2. Bibliometric dataset and 3. Researcher dataset and carried out descriptive analysis.
Results
Of the 126 articles retrieved, 119 articles were selected for inclusion in the study. The tally increased to 133 articles after a secondary search. Based on the information available in the articles, we identified a total of 91 unique research resources. We observed that most of the resources were Registries (62/91) and Databases ( 23/91) and were primarily located in Maharashtra (19/91) followed by Tamil Nadu (11/91), Chandigarh (8/91) and Kerala (7/91) States. These resources primarily collected data on Cancer (44/91), Stroke (5/91) and Diabetes (4/91). Most of these resources were Institutional (38/91) and Regional resources (35/91) located in Government owned and managed Academic Institutes/Hospitals (57/91) or Privately owned and managed non – Academic Institutes/Hospitals (14/91). Data from the Population based Cancer Registry, Mumbai was used in 41 peer reviewed publications followed by Population based Cancer Registry, Chennai (17) and Rural Cancer Registry Barshi (14). Most of the articles were published in International journals (139/193) that had an impact factor of 0–1.99 (43/91) and received an average of 0–20 citations (55/91). We identified 193 researchers who are mainly located in Maharashtra (37/193) and Tamil Nadu (24/193) states and Southern (76/193) and Western zones (47/193). They were mainly affiliated to Government owned & managed Academic Institutes /Hospitals (96/193) or privately owned and managed Academic Institutes/ Hospitals (35/193).
Conclusions
Given the importance of Outcomes research, relevant resources should be supported and encouraged which would help in the generation of important healthcare data that can guide health and research policy. Clarity about the distribution of outcomes research resources can facilitate future resource and funding allocation decisions for policy makers as well as help them measure research performance over time.
Electronic supplementary material
The online version of this article (doi:10.1186/2193-1801-2-518) contains supplementary material, which is available to authorized users.
doi:10.1186/2193-1801-2-518
PMCID: PMC3804670  PMID: 24171151
Outcomes research; Research resources; India
16.  BCDB ‐ A database for breast cancer research and information 
Bioinformation  2010;5(1):1-3.
In pursuit of a better updated source including ‘omics’ information for breast cancer, Breast Cancer Database (BCDB) has been developed to provide the researcher with the quick overview of the Breast cancer disease and other relevant information. This database comprises of myriad of information about genes involved in breast cancer, its functions and drug molecules which are currently being used in the treatment of breast cancer. The data available in BCDB is retrieved from the biomedical research literature. It facilitates the user to search information on gene, its location in chromosome, functions and its importance in cancer diseases. Broadly, this can be queried by giving gene name, protein name and drug name. This database is platform independent, user friendly and freely accessible through internet. The data present in BCDB is directly linked to other on-line resources such as NCBI, PDB and PubMed. Hence, it can act as a complete web resource comprising gene sequences, drug structures and literature information related to breast cancer, which is not available in any other breast cancer database.
Availability
The database is freely available at http://122.165.25.137/bioinfo/breastcancerdb/
PMCID: PMC3039995  PMID: 21346869
Breast cancer; database; genes; protein; drug; PDB structure; FASTA
17.  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
18.  An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow 
BMC Bioinformatics  2009;10:252.
Background
Genomic analysis, particularly for less well-characterized organisms, is greatly assisted by performing comparative analyses between different types of genome maps and across species boundaries. Various providers publish a plethora of on-line resources collating genome mapping data from a multitude of species. Datasources range in scale and scope from small bespoke resources for particular organisms, through larger web-resources containing data from multiple species, to large-scale bioinformatics resources providing access to data derived from genome projects for model and non-model organisms. The heterogeneity of information held in these resources reflects both the technologies used to generate the data and the target users of each resource. Currently there is no common information exchange standard or protocol to enable access and integration of these disparate resources. Consequently data integration and comparison must be performed in an ad hoc manner.
Results
We have developed a simple generic XML schema (GenomicMappingData.xsd – GMD) to allow export and exchange of mapping data in a common lightweight XML document format. This schema represents the various types of data objects commonly described across mapping datasources and provides a mechanism for recording relationships between data objects. The schema is sufficiently generic to allow representation of any map type (for example genetic linkage maps, radiation hybrid maps, sequence maps and physical maps). It also provides mechanisms for recording data provenance and for cross referencing external datasources (including for example ENSEMBL, PubMed and Genbank.). The schema is extensible via the inclusion of additional datatypes, which can be achieved by importing further schemas, e.g. a schema defining relationship types. We have built demonstration web services that export data from our ArkDB database according to the GMD schema, facilitating the integration of data retrieval into Taverna workflows.
Conclusion
The data exchange standard we present here provides a useful generic format for transfer and integration of genomic and genetic mapping data. The extensibility of our schema allows for inclusion of additional data and provides a mechanism for typing mapping objects via third party standards. Web services retrieving GMD-compliant mapping data demonstrate that use of this exchange standard provides a practical mechanism for achieving data integration, by facilitating syntactically and semantically-controlled access to the data.
doi:10.1186/1471-2105-10-252
PMCID: PMC2743669  PMID: 19682365
19.  Expanding and Enhancing Access to the Sequence Read Archive (SRA) Through a Complementary New Web-based Mirror 
Public institutions such as the National Center for Biotechnology Information (NCBI) have made tremendous investments in generating and archiving a wide array of valuable genomic data for use by the research community. Expanding access to these valuable public data and streamlining the ability to integrate them into data management tools and powerful analyses, will further expedite their use and value in medical research, discovery and applications.
Teaming up with Google, DNAnexus has developed a complementary hosted mirror of the NCBI's Sequence Read Archive (SRA) that provides researchers an additional way to access these important datasets. This freely accessible resource provides a new web-based user interface built using the latest “cloud” technologies and genomic data standards. As the most comprehensive archive of publicly available next-generation sequencing data, the SRA is an important resource to researchers around the world. The SRA remains the single best source of useful sequence data from research initiatives such as the 1,000 Genomes Project and institutions like the Broad Institute, Washington University, and the Wellcome Trust Sanger Institute.
Here we discuss our work with the NCBI and Google to create a complementary mirror of the SRA available at sra.dnanexus.com. Through a typical user scenario, we will discuss the underlying data processing pipeline, key features of the new web-based interface that enables researchers to quickly identify and browse datasets of interest, link-outs to PubMed references, and integration of those data into an analysis workflow for hypothesis generation.
PMCID: PMC3630627
20.  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

21.  Disability in activities of daily living, depression, and quality of life among older medical ICU survivors: a prospective cohort study 
Background
Accurate measurement of quality of life in older ICU survivors is difficult but critical for understanding the long-term impact of our treatments. Activities of daily living (ADLs) are important components of functional status and more easily measured than quality of life (QOL). We sought to determine the cross-sectional associations between disability in ADLs and QOL as measured by version one of the Short Form 12-item Health Survey (SF-12) at both one month and one year post-ICU discharge.
Methods
Data was prospectively collected on 309 patients over age 60 admitted to the Yale-New Haven Hospital Medical ICU between 2002 and 2004. Among survivors an assessment of ADL's and QOL was performed at one month and one-year post-ICU discharge. The SF-12 was scored using the version one norm based scoring with 1990 population norms. Multivariable regression was used to adjust the association between ADLs and QOL for important covariates.
Results
Our analysis of SF-12 data from 110 patients at one month post-ICU discharge showed that depression and ADL disability were associated with decreased QOL. Our model accounted for 17% of variability in SF12 physical scores (PCS) and 20% of variability in SF12 mental scores (MCS). The mean PCS of 37 was significantly lower than the population mean whereas the mean MCS score of 51 was similar to the population mean. At one year mean PCS scores improved and ADL disability was no longer significantly associated with QOL. Mortality was 17% (53 patients) at ICU discharge, 26% (79 patients) at hospital discharge, 33% (105 patients) at one month post ICU admission, and was 45% (138 patients) at one year post ICU discharge.
Conclusions
In our population of older ICU survivors, disability in ADLs was associated with reduced QOL as measured by the SF-12 at one month but not at one year. Although better markers of QOL in ICU survivors are needed, ADLs are a readily observable outcome. In the meantime, clinicians must try to offer realistic estimates of prognosis based on available data and resources are needed to assist ICU survivors with impaired ADLs who wish to maintain their independence. More aggressive diagnosis and treatment of depression in this population should also be explored as an intervention to improve quality of life.
doi:10.1186/1477-7525-9-9
PMCID: PMC3041645  PMID: 21294911
22.  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
23.  Evaluation of internet access and utilization by medical students in Lahore, Pakistan 
Background
The internet is increasingly being used worldwide in imparting medical education and improving its delivery. It has become an important tool for healthcare professionals training but the data on its use by medical students in developing countries is lacking with no study on the subject from Pakistan. This study was, therefore, carried out with an aim to evaluate the pattern of internet access and utilization by medical students in Pakistan.
Methods
A structured pre-tested questionnaire was administered to a group of 750 medical students in clinical years studying at various public and private medical colleges in Lahore. The questions were related to patterns of internet access, purpose of use and self reported confidence in performing various internet related tasks, use of health related websites to supplement learning and the problems faced by students in using internet at the institution.
Results
A total of 532 medical students (70.9%) returned the questionnaire. The mean age of study participants was 21.04 years (SD 1.96 years). Majority of the respondents (84.0%) reported experience with internet use. About half of the students (42.1%) were using internet occasionally with 23.1%, 20.9% and 13.9% doing so frequently, regularly and rarely respectively. About two third of the students (61.0%) stated that they use internet for both academic and professional activities. Most of the participants preferred to use internet at home (70.5%). Self reported ability to search for required article from PubMed and PakMedinet was reported by only 34.0% of the entire sample. Students were moderately confident in performing various internet related tasks including downloading medical books from internet, searching internet for classification of diseases and downloading full text article. Health related websites were being accessed by 55.1% students to supplement their learning process. Lack of time, inadequate number of available computers and lack of support from staff were cited as the most common problems faced by students while accessing internet in the institution premises. There were significant differences among male and female students with respect to the place of internet use (p = 0.001) and the ability to search online databases for required articles (p = 0.014).
Conclusions
Majority of the medical students in this study had access to internet and were using it for both academic and personal reasons. Nevertheless, it was seen that there is under utilization of the potential of internet resources to augment learning. Increase in awareness, availability of requisite facilities and training in computing skills are required to enable better utilization of digital resources of digital resources by medical students.
doi:10.1186/1472-6947-11-37
PMCID: PMC3119193  PMID: 21619707
24.  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
25.  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

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