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

A temporal examination of calcium signaling in cancer- from tumorigenesis, to immune evasion, and metastasis

Abstract Background Although the study of calcium (Ca2+) is classically associated with excitable cells such as myocytes or neurons, the ubiquity of this essential element in all cellular processes has led to interest in other cell types. The importance of Ca2+ to apoptosis, cell signaling, and immune activation is of special import in cancer. Main Here we review the current understanding of Ca2+ in each of these processes vital to the initiation, spread, and drug resistance of malignancies. We describe the involvement of Ca2+, and Ca2+ related proteins in cell cycle checkpoints and Ca2+ dependent apoptosis and discuss their roles in cellular immortalization. The role of Ca2+ in inter-cellular communication is also discussed in relevance to tumor-stromal communication, angiogenesis, and tumor microinvasion. The role that Ca2+ plays in immune surveillance and evasion is also addressed. Finally, we discuss the possibility of targeting Ca2+ singling to address the most pressing topics of cancer treatment: metastatic disease and drug resistance. Conclusion This review discusses the current understanding of Ca2+ in cancer. By addressing Ca2+ facilitated angiogenesis, immune evasion, metastasis, and drug resistance, we anticipate future avenues for development of Ca2+ as a nexus of therapy