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

DIETARY EXPOSURE TO NITRITE AND NITROSAMINES AND RISK OF NASOPHARYNGEAL CARCINOMA IN TAIWAN

Previous studies of nasopharyngeal carcinoma (NPC) have found elevated risks with higher consumption of salted fish and preserved foods, particularly during childhood. These foods can contain high levels of nitrosamines; however, most studies have not estimated exposure to nitrosamines directly. We conducted a case-control study in Taiwan to evaluate dietary intakes and NPC risk. A total of 375 cases( 99% response rate) and 327 controls (88% response rate) were interviewed about their diet as an adult and at age 10 using a food-frequency questionnaire. We interviewed mothers of participants about their child's diet at age 10, age 3 and during weaning and the mother's diet while she was breast-feeding. Mothers of 96 cases and 120 controls were interviewed. Nitrosamine and nitrite levels were assigned to 66 foods based on published values. Intake of nitrosamines and nitrite as an adult was not associated with risk of NPC. High intakes of nitrosamines and nitrite during childhood and weaning were associated with increased risks of NPC for foods other than soy products. Adjusted odds ratios for the highest quartile were 2.2 [95% confidence interval (CI) 0.8- 5.6] for age 10, 2.6 (95% CI 1.0-7.0) for age 3 and 3.9 (95 % CI 1.4-10.4) for weaning diet. Intakes of nitrite and nitrosamines from soybean products during childhood and weaning were inversely associated with risk. Soybeans contain known inhibitors of nitrosation, and thus may explain the inverse association we observed. Our results suggest that nitrosamine and nitrite intake during childhood may play a role in the development of NPC. Int. J. Cancer 86:603-609, 2000. Published 2000 Wiley-Liss, Inc

NO ASSOCIATION BETWEEN GENETIC POLYMORPHISMS OF CYP1A1, GSTM1, GSTT 1, GSTP1, NAT2, AND NASOPHARYNGEAL CARCINOMA IN TAIWAN

NPC2 is rare in most populations around the world but common in southern China and Southeast Asia. Both genetic and environmental factors are purported to account for the development of NPC. Many Phase I and Phase II enzymes get involved in the metabolism of carcinogens. Some of these enzymes are polymorphic in genotypes that show considerable variation in their activities, which, in turn, determine individual susceptibility to cancer risk (1) . No studies to date have examined simultaneously the association between genetic polymorphisms of multiple xenobiotic-metabolizing enzymes and NPC. We have previously reported an association between genetic polymorphism in the CYP2E1 gene and risk of NPC (2) . In this study, we examine the association with NPC of genetic polymorphisms of CYP1A1, GSTM1, GSTT1, GSTP1, and NAT2