Studying PubMed usages in the field for complex problem solving: Implications for tool design

Long-term evaluation of the seroprevalence of SARS-CoV-2 IgG and IgM antibodies in recovered patients: a meta-analysis

Estimating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) -specific immunoglobulin G (IgG) immunoglobulin M (IgM) antibodies are increasingly important for tracking the spread of infection and defining herd immunity barrier and individual immunization levels in the ongoing coronavirus disease 2019 (COVID-19) pandemic. Therefore, we conducted the present systematic review and meta-analysis to evaluate the seroprevalence of SARS-CoV-2 IgM and IgG antibodies of recovered COVID-19 patients in long-term follow-up studies. A systematic search of the MEDLINE, Embase, COVID-19 Primer, PubMed, CNKI, and the Public Health England library databases was conducted. Twenty-fourth eligible studies were included. Meta-analysis showed that 27% (95%CI: 0.04-0.49) and 66% (95%CI:0.47-0.85) were seropositive for SARS-CoV-2 IgM and IgG, respectively, while in long-term 12 months following up studies, the seroprevalences of IgM antibody (17%) decreased and IgG antibody (75%) was higher than 6 months follow-up patients. However, due to the limited number of relevant studies, the high level of heterogeneity, and the large gap in studies conducted, the findings of our study may not accurately reflect the true seroprevalence status of SARS-CoV-2 infection. Nevertheless, sequential vaccination or booster immunization is considered to be a necessary long-term strategy to sustain the fight against the pandemic.

Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing

BACKGROUND

Structured electronic health records are a rich resource for identifying novel correlations, such as co-morbidities and adverse drug reactions. For drug development and better understanding of biomedical phenomena, such correlations need to be supported by viable hypotheses about the mechanisms involved, which can then form the basis of experimental investigations.

METHODS

In this study, we demonstrate the use of discovery browsing, a literature-based discovery method, to generate plausible hypotheses elucidating correlations identified from structured clinical data. The method is supported by Semantic MEDLINE web application, which pinpoints interesting concepts and relevant MEDLINE citations, which are used to build a coherent hypothesis.

RESULTS

Discovery browsing revealed a plausible explanation for the correlation between epilepsy and inflammatory bowel disease that was found in an earlier population study. The generated hypothesis involves interleukin-1 beta (IL-1 beta) and glutamate, and suggests that IL-1 beta influence on glutamate levels is involved in the etiology of both epilepsy and inflammatory bowel disease.

CONCLUSIONS

The approach presented in this paper can supplement population-based correlation studies by enabling the scientist to identify literature that may justify the novel patterns identified in such studies and can underpin basic biomedical research that can lead to improved treatments and better healthcare outcomes.

Informatics Support for Basic Research in Biomedicine

Informatics methodologies exploit computer-assisted techniques to help biomedical researchers manage large amounts of information. In this paper, we focus on the biomedical research literature (MEDLINE). We first provide an overview of some text mining techniques that offer assistance in research by identifying biomedical entities (e.g., genes, substances, and diseases) and relations between them in text.We then discuss Semantic MEDLINE, an application that integrates PubMed document retrieval, concept and relation identification, and visualization, thus enabling a user to explore concepts and relations from within a set of retrieved citations. Semantic MEDLINE provides a roadmap through content and helps users discern patterns in large numbers of retrieved citations. We illustrate its use with an informatics method we call "discovery browsing," which provides a principled way of navigating through selected aspects of some biomedical research area. The method supports an iterative process that accommodates learning and hypothesis formation in which a user is provided with high level connections before delving into details.As a use case, we examine current developments in basic research on mechanisms of Alzheimer's disease. Out of the nearly 90 000 citations returned by the PubMed query "Alzheimer's disease," discovery browsing led us to 73 citations on sortilin and that disorder. We provide a synopsis of the basic research reported in 15 of these. There is wide-spread consensus among researchers working with a range of animal models and human cells that increased sortilin expression and decreased receptor expression are associated with amyloid beta and/or amyloid precursor protein.

Use of scientific social networking to improve the research strategies of PubMed readers

Background

Keeping up with journal articles on a daily basis is an important activity of scientists engaged in biomedical research. Usually, journal articles and papers in the field of biomedicine are accessed through the Medline/PubMed electronic library. In the process of navigating PubMed, researchers unknowingly generate user-specific reading profiles that can be shared within a social networking environment. This paper examines the structure of the social networking environment generated by PubMed users.

Methods

A web browser plugin was developed to map [in Medical Subject Headings (MeSH) terms] the reading patterns of individual PubMed users.

Results

We developed a scientific social network based on the personal research profiles of readers of biomedical articles. A browser plugin is used to record the digital object identifier or PubMed ID of web pages. Recorded items are posted on the activity feed and automatically mapped to PubMed abstract. Within the activity feed a user can trace back previously browsed articles and insert comments. By calculating the frequency with which specific MeSH occur, the research interests of PubMed users can be visually represented with a tag cloud. Finally, research profiles can be searched for matches between network users.

Conclusions

A social networking environment was created using MeSH terms to map articles accessed through the Medline/PubMed online library system. In-network social communication is supported by the recommendation of articles and by matching users with similar scientific interests. The system is available at http://bioknol.org/en/.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-016-1920-y) contains supplementary material, which is available to authorized users.

Untangling search task complexity and difficulty in the context of interactive information retrieval studies

Purpose

– One core element of interactive information retrieval (IIR) experiments is the assignment of search tasks. The purpose of this paper is to provide an analytical review of current practice in developing those search tasks to test, observe or control task complexity and difficulty.

Design/methodology/approach

– Over 100 prior studies of IIR were examined in terms of how each defined task complexity and/or difficulty (or related concepts) and subsequently interpreted those concepts in the development of the assigned search tasks.

Findings

– Search task complexity is found to include three dimensions: multiplicity of subtasks or steps, multiplicity of facets, and indeterminability. Search task difficulty is based on an interaction between the search task and the attributes of the searcher or the attributes of the search situation. The paper highlights the anomalies in our use of these two concepts, concluding with suggestions for future methodological research related to search task complexity and difficulty.

Originality/value

– By analyzing and synthesizing current practices, this paper provides guidance for future experiments in IIR that involve these two constructs.