Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Fibroblast Growth Factor-2 Enhances Proliferation and Delays Loss of Chondrogenic Potential in Human Adult Bone-Marrow-Derived Mesenchymal Stem Cells

We compared human mesenchymal stem cells (hMSCs), expanded long term with and without fibroblast growth factor (FGF) supplementation, with respect to proliferation, and the ability to undergo chondrogenesis in vitro. hMSCs expanded in FGF-supplemented medium proliferated more rapidly than the control cells. Aggregates of FGF-treated cells exhibited chondrogenic differentiation at all passages tested although, in some preparations, differentiation was diminished after seventh passage. Aggregates made with control cells differentiated along the chondrogenic lineage after first passage but exhibited only marginal differentiation after fourth and failed to form cartilage after seventh passage. Microarray analysis of gene expression identified 334 transcripts differentially expressed in fourth passage control cells that had reduced chondrogenic potential, compared with the fourth passage FGF-treated cells that retained this capacity, and 243 transcripts that were differentially expressed when comparing them to the first passage control cells that were also capable of differentiating into chondrocytes. The intersection of these analyses yielded 49 transcripts differentially expressed in cells that exhibited chondrogenic differentiation in vitro compared with the cells that did not. Among these, angiopoietin 1, secreted frizzled-related protein 1, and six transmembrane epithelial antigen of the prostate 1 appear to be of higher relevance. These preliminary data must now be validated to verify whether different gene expression profiles translate into functional differences. In summary, these findings suggest that the chondrogenic potential of hMSCs is vulnerable to cell expansion and that care should be exercised when expanding these cells for cartilage tissue engineering applications. Supplementation with FGF-2 allows reaching target cell numbers more rapidly and extends the level of expansion within which these cells are useful for tissue-engineered cartilage repair