Proportional odds ratio model for comparison of diagnostic tests in meta-analysis

BACKGROUND: Consider a meta-analysis where a 'head-to-head' comparison of diagnostic tests for a disease of interest is intended. Assume there are two or more tests available for the disease, where each test has been studied in one or more papers. Some of the papers may have studied more than one test, hence the results are not independent. Also the collection of tests studied may change from one paper to the other, hence incomplete matched groups. METHODS: We propose a model, the proportional odds ratio (POR) model, which makes no assumptions about the shape of OR(p), a baseline function capturing the way OR changes across papers. The POR model does not assume homogeneity of ORs, but merely specifies a relationship between the ORs of the two tests. One may expand the domain of the POR model to cover dependent studies, multiple outcomes, multiple thresholds, multi-category or continuous tests, and individual-level data. RESULTS: In the paper we demonstrate how to formulate the model for a few real examples, and how to use widely available or popular statistical software (like SAS, R or S-Plus, and Stata) to fit the models, and estimate the discrimination accuracy of tests. Furthermore, we provide code for converting ORs into other measures of test performance like predictive values, post-test probabilities, and likelihood ratios, under mild conditions. Also we provide code to convert numerical results into graphical ones, like forest plots, heterogeneous ROC curves, and post test probability difference graphs. CONCLUSIONS: The flexibility of POR model, coupled with ease with which it can be estimated in familiar software, suits the daily practice of meta-analysis and improves clinical decision-making

E-Learning: From A Pedagogical Perspective

The steady growing innovations in the area of information and communication technology have raised new concepts and possibilities in different life aspects. In the field of further education and professional training, electronic learning and Web-based education are perhaps the most prominent ones. Proponents of this technology claim that e-learning courses are at least as effective as corresponding traditional ones, and therefore sometimes a very good substitute for it. Although there are so many similarities between traditional and e-learning systems, confronting the extended range of e-learning users -with very different prior knowledge of the domain, backgrounds, learning styles, interests and preferences- is no more possible with the “one-size-fits-all” approach. Hence, creation and management of instructional content would be the major hazard in e-learning industry. Contents should be provided considering social, cultural and pedagogical characteristics of the learners. E-learning covers a wide set of applications and processes. With such an extended scope, covering number of available e-learning tools is extensive. Though, in recent years, features and capabilities of authoring tools have been drastically improved. Concepts such as “adapting to the needs of learners” and “personalized content” make authoring tools play a more prominent role in the process of creating learning contents. In this paper, we propose a new pedagogical perspective in web-based learning environments. This perspective explores the most prominent opportunities of the information technology era, in order to ensure a more meaningful learning. Advantages, limitations and particularly deficiencies of e-learning systems are investigated based on this perspective. Also, in order to cover the importance of authoring tools in the performance of e-learning systems, capabilities and limitations of current available authoring tools are comparatively studied. These comparisons are based on criteria such as compatibility with e-learning standards, the amount of time and cost needed for the instructional design and potential features. Outcomes of the study emphasize on the importance of the learning variables such as cognitive, social and affective learners’ characteristics, which play a critical role in the design and implementation of web-based learning systems. These outcomes would certainly be of significant help with enhancing the decision making procedure for managers and presidents of learning areas, which may be overwhelmed by all the technology decisions they have to make, the number of choices available, and the terminology they may not be familiar with. These outcomes would basically lead to determining basic factors of learner satisfaction and therefore improving educational performance

Geographic bias related to geocoding in epidemiologic studies

BACKGROUND: This article describes geographic bias in GIS analyses with unrepresentative data owing to missing geocodes, using as an example a spatial analysis of prostate cancer incidence among whites and African Americans in Virginia, 1990–1999. Statistical tests for clustering were performed and such clusters mapped. The patterns of missing census tract identifiers for the cases were examined by generalized linear regression models. RESULTS: The county of residency for all cases was known, and 26,338 (74%) of these cases were geocoded successfully to census tracts. Cluster maps showed patterns that appeared markedly different, depending upon whether one used all cases or those geocoded to the census tract. Multivariate regression analysis showed that, in the most rural counties (where the missing data were concentrated), the percent of a county's population over age 64 and with less than a high school education were both independently associated with a higher percent of missing geocodes. CONCLUSION: We found statistically significant pattern differences resulting from spatially non-random differences in geocoding completeness across Virginia. Appropriate interpretation of maps, therefore, requires an understanding of this phenomenon, which we call "cartographic confounding.

Air Travel and Venous Thromboembolism: A Systematic Review

CONTEXT: Despite multiple attempts to document and quantify the danger of venous thromboembolism (VTE) following prolonged travel, there is still uncertainty about the magnitude of risk and what can be done to lower it. OBJECTIVES: To review the methodologic strength of the literature, estimate the risk of travel-related VTE, evaluate the efficacy of preventive treatments, and develop evidence-based recommendations for practice. DATA SOURCES: Studies identified from MEDLINE from 1966 through December 2005, supplemented by a review of the Cochrane Central Registry of Controlled Trials, the Database of Abstracts of Reviews of Effects, and relevant bibliographies. STUDY SELECTION: We included all clinical studies that either reported primary data concerning travel as a risk factor for VTE or tested preventive measures for travel-related VTE. DATA EXTRACTION AND ANALYSIS: Two reviewers reviewed each study independently to assess inclusion criteria, classify research design, and rate methodologic features. The effect of methodologic differences, VTE risk, and travel duration on VTE rate was evaluated using a logistic regression model. DATA SYNTHESIS: Twenty-four published reports, totaling 25 studies, met inclusion criteria (6 case-control studies, 10 cohort studies, and 9 randomized controlled trials). Method of screening for VTE [screening ultrasound compared to usual clinical care, odds ratio (OR) 390], outcome measure [all VTE compared to pulmonary embolism (PE) only, OR 21], duration of travel (<6 hours compared to 6–8 hours, OR 0.011), and clinical risk (“higher” risk travelers compared to “lower,” OR 3.6) were significantly related to VTE rate. Clinical VTE after prolonged travel is rare [27 PE per million flights diagnosed through usual clinical care, 0.05% symptomatic deep venous thrombosis (DVT) diagnosed through screening ultrasounds], but asymptomatic thrombi of uncertain clinical significance are more common. Graduated compression stockings prevented travel-related VTE (P < 0.05 in 4 of 6 studies), aspirin did not, and low-molecular-weight heparin (LMWH) showed a trend toward efficacy in one study. CONCLUSIONS: All travelers, regardless of VTE risk, should avoid dehydration and frequently exercise leg muscles. Travelers on a flight of less than 6 hours and those with no known risk factors for VTE, regardless of the duration of the flight, do not need DVT prophylaxis. Travelers with 1 or more risk factors for VTE should consider graduated compression stockings and/or LMWH for flights longer than 6 hours

Unobtrusive Observation of Team Learning Attributes in Digital Learning

This article presents a new framework for unobtrusive observation analytics of knowledge and skills-in-action through continuous collection of data from individuals while they interact with digital assets either as individuals or on problem-solving teams. The framework includes measures of the skill and knowledge areas of collaboration, creativity, personal learning, problem solving, and global sustainability, which are observed during natural production and use of communications, intentional artifacts, and resources in a digital learning space designed for self-directed and team-based learning challenges. The article describes the digital context for data collection and shows some example data and analyses

PubMed and beyond: a survey of web tools for searching biomedical literature

The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field

Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text

<p>Abstract</p> <p>Background</p> <p>Pharmacogenomics studies the relationship between genetic variation and the variation in drug response phenotypes. The field is rapidly gaining importance: it promises drugs targeted to particular subpopulations based on genetic background. The pharmacogenomics literature has expanded rapidly, but is dispersed in many journals. It is challenging, therefore, to identify important associations between drugs and molecular entities – particularly genes and gene variants, and thus these critical connections are often lost. Text mining techniques can allow us to convert the free-style text to a computable, searchable format in which pharmacogenomic concepts (such as genes, drugs, polymorphisms, and diseases) are identified, and important links between these concepts are recorded. Availability of full text articles as input into text mining engines is key, as literature abstracts often do not contain sufficient information to identify these pharmacogenomic associations.</p> <p>Results</p> <p>Thus, building on a tool called Textpresso, we have created the Pharmspresso tool to assist in identifying important pharmacogenomic facts in full text articles. Pharmspresso parses text to find references to human genes, polymorphisms, drugs and diseases and their relationships. It presents these as a series of marked-up text fragments, in which key concepts are visually highlighted. To evaluate Pharmspresso, we used a gold standard of 45 human-curated articles. Pharmspresso identified 78%, 61%, and 74% of target gene, polymorphism, and drug concepts, respectively.</p> <p>Conclusion</p> <p>Pharmspresso is a text analysis tool that extracts pharmacogenomic concepts from the literature automatically and thus captures our current understanding of gene-drug interactions in a computable form. We have made Pharmspresso available at <url>http://pharmspresso.stanford.edu</url>.</p