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

The effect of high-dose vitamin A supplementation given with bacille Calmette-Guérin vaccine at birth on infant rotavirus infection and diarrhea: a randomized prospective study from Guinea-Bissau

Background. Prophylactic vitamin A supplementation (VAS) reduces mortality and may reduce morbidity associated with diarrhea in children 16 months of age. Rotavirus is the most common cause of acute dehydrating diarrhea among children worldwide. Methods. In a randomized placebo-controlled study of 50,000 IU of vitamin A versus placebo given with bacille Calmette-Guerin vaccine at birth, 287 infants were followed up with weekly interviews and stool sample obtainment to test the hypothesis that VAS reduced the risk of rotavirus infection. Results. VAS was associated with increased risk of rotavirus infection and diarrhea (incidence rate ratio [IRR] of infection, 1.72 [95% confidence interval (CI), 1.04-2.85]; IRR of diarrhea, 3.74 [95% CI, 1.40-9.98]) among children 6 months of age (IRR, 1.84; 95% CI, 0.96-3.55). Conclusion. VAS at birth did not reduce rotavirus morbidity. The effect of VAS on nonrotavirus diarrhea may differ by sex, being more beneficial in boys.Host-parasite interactio