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

Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features

The value of genome-wide over targeted driver analyses for predicting clinical outcomes of cancer patients is debated. Here, we report the whole-genome sequencing of 485 chronic lymphocytic leukemia patients enrolled in clinical trials as part of the United Kingdom’s 100,000 Genomes Project. We identify an extended catalog of recurrent coding and noncoding genetic mutations that represents a source for future studies and provide the most complete high-resolution map of structural variants, copy number changes and global genome features including telomere length, mutational signatures and genomic complexity. We demonstrate the relationship of these features with clinical outcome and show that integration of 186 distinct recurrent genomic alterations defines five genomic subgroups that associate with response to therapy, refining conventional outcome prediction. While requiring independent validation, our findings highlight the potential of whole-genome sequencing to inform future risk stratification in chronic lymphocytic leukemia

Not Available

Field application of Rice husk ash and inmidazole is beneficial to rice plantSilicon (Si) has been implicated to reduce damage by rice pests. In this study we validate the field efficacy of rice husk ash (RHA) and imidazole, alone and in combination, against damage by yellow stem borer (YSB) under field conditions for two seasons in five rice cultivars. Field application of RHA and imidazole, either alone or in combination, enhanced Si deposition (43–59.8 mg g −1 ) in stem tissues of rice plants as compared to untreated control (30.2 mg g −1 ). Deposited Si caused significant wearing of mandible incisors, and lowered larval density, thereby decreasing YSB damage and increasing the grain yield significantly. RHA and imidazole did not alter the total sugars and total phenol content in rice cultivars. Field application of imidazole along with RHA at vegetative phase and again at booting stage was on par with insecticidal treatment (carbofuran 3G) with respect to per cent damage, larval density and grain yield. The B: C ratio in the Si treatments varied from 1.16 to 1.31 and T4-RHA +imidazole (applied twice) was at par with one granular insecticide application (1.32) but higher than the untreated control (1.0). RHA and imidazole can be integrated as one of the eco-friendly components in the present scenario of climate change for the management of YSB in rice.Not Availabl