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

Glycan analysis of colorectal cancer samples reveals stage-dependent changes in CEA glycosylation patterns

Abstract Background Carcinoembryonic antigen (CEA) is a glycoprotein associated with colorectal cancer (CRC). While the functions of its gene and protein have been fully characterized, its post-translational modifications in the context of CRC development remain undefined. Methods To show the correlation between the different stages of CRC development and changes in the glycosylation patterns of CEA, we analyzed CEA in tumor tissues (CEA-T) and paired tumor-adjacent normal tissues (CEA-A) from 53 colorectal cancer patients using a high-density lectin microarray containing 56 plant lectins. Results We detected higher expression levels of fucose, mannose and Thomsen–Friedenreich antigen, and lower expression levels of N-acetylgalactosamine, N-acetylglucosamine, galactose, branched and bisecting N-glycans on CEA in the tumor tissues relative to the tumor-adjacent normal tissues. Furthermore, a combinatorial assessment of 9 lectins is sufficient to distinguish CRC tumor tissues from tumor-adjacent normal tissues with 83% sensitivity and ~ 90% specificity. Moreover, the levels of N-acetylgalactosamine, mannose, galactose, N-acetylglucosamine on CEA showed a downward trend after first experiencing an increase at Stage II with the stages of CRC. Conclusions Our insights into the changing CEA glycosylation patterns and their role in the development of CRC highlight the importance of glycan variants on CEA for early clinical detection and staging of CRC

MOESM2 of Glycan analysis of colorectal cancer samples reveals stage-dependent changes in CEA glycosylation patterns

Additional file 2. 31 lectins bind different concentrations of CEA

MOESM1 of Glycan analysis of colorectal cancer samples reveals stage-dependent changes in CEA glycosylation patterns

Additional file 1: Table S1. Lectin used in this study

MOESM4 of Glycan analysis of colorectal cancer samples reveals stage-dependent changes in CEA glycosylation patterns

Additional file 4: Table S2. The concentration of CEA of CRC patients; Figure S1. The relationship between CEA concentration and CRC stages

Knocking Down the Expression of GMPase Gene <i>OsVTC1-1</i> Decreases Salt Tolerance of Rice at Seedling and Reproductive Stages

<div><p>Salinity is a severe environmental stress that greatly impairs production of crops worldwide. Previous studies have shown that GMPase plays an important role in tolerance of plants to salt stress at vegetative stage. However, the function of GMPase in plant responses to salt stress at reproductive stage remains unclear. Studies have shown that heterologous expression of rice GMPase <i>OsVTC1-1</i> enhanced salt tolerance of tobacco seedlings, but the native role of <i>OsVTC1-1</i> in salt stress tolerance of rice is unknown. To illustrate the native function of GMPase in response of rice to salt stress, <i>OsVTC1-1</i> expression was suppressed using RNAi-mediated gene silencing. Suppressing <i>OsVTC1-1</i> expression obviously decreased salt tolerance of rice varieties at vegetative stage. Intriguingly, grain yield of <i>OsVTC1-1</i> RNAi rice was also significantly reduced under salt stress, indicating that <i>OsVTC1-1</i> plays an important role in salt tolerance of rice at both seedling and reproductive stages. <i>OsVTC1-1</i> RNAi rice accumulated more ROS under salt stress, and supplying exogenous ascorbic acid restored salt tolerance of <i>OsVTC1-1</i> RNAi lines, suggesting that <i>OsVTC1-1</i> is involved in salt tolerance of rice through the biosynthesis regulation of ascorbic acid. Altogether, results of present study showed that rice GMPase gene <i>OsVTC1-1</i> plays a critical role in salt tolerance of rice at both vegetative and reproductive stages through AsA scavenging of excess ROS.</p></div

<i>OsVTC1-1</i> plays an important role in the response of salt-tolerant rice varieties.

<p>(A), phenotypes of F1 hybrid rice plants under salt stress. NJ16 represents salt-tolerant rice landrace Ningjing16; NJ16/RI1-3 represents F1 hybrid of Ningjing16 with <i>OsVTC1-1</i> RNA interference line RI1-3; NJ16/ZH17 represents F1 plants of Ningjing16 and Zhonghua17, which were used as controls. ZD13 indicates the salt-tolerant rice landrace Zhongdao13; ZD13/RI1-3 indicates F1 plants of Zhongdao13 and <i>OsVTC1-1</i> RI1-3; ZD13/ZH17 indicates F1 plants of Zhongdao13 and Zhonghua17, which were used as controls. Ningjing16 and Zhongdao13 were used as the female parents. Control indicates that plants were grown under normal conditions, and NaCl indicates that four-week rice seedlings were treated with 150 mM NaCl solution for another ten days. (B), percentage survival rates (Percentage is the ratio of number of plants with green new leaves to number of total plants) of F1 hybrid rice seedlings after salt stress treatment in (A). About 50~60 seedlings were uses in each experiment. The bars represent SD (±) of two independent assays, and the asterisk indicates results significantly different from control (**P<0.01 and *P<0.05). Significance was evaluated using the <i>t</i>-test.</p

Overexpression of <i>OsVTC1-1</i> enhances the tolerance of <i>Arabidopsis</i> to salt stress.

<p>(A), phenotypes of <i>OsVTC1-1</i> overexpressing <i>Arabidopsis</i> under salt stress. Control indicates that plants were grown under normal conditions, and NaCl indicates that <i>Arabidopsis</i> seedlings were treated with 150 mM NaCl for ten days. (B), the percentage survival rates of <i>OsVTC1-1</i> overexpressing lines after salt treatment in (A). OE-v represents <i>vtc1-1</i> plants transformed with the pCAMBIA1307 blank vector. OE1-1 and OE1-3 indicate different overexpression lines of <i>OsVTC1-1</i> in <i>vtc1-1</i> background. WT represents wild-type Col-0 <i>Arabidopsis</i>. About 70~80 seedlings were uses in each experiment. The bars represent SE (±) of three independent assays, and the asterisk indicates results significantly different from <i>vtc1-1</i> (**P<0.01 and *P<0.05). Significance was evaluated using the <i>t</i>-test.</p

Decreasing the expression of <i>OsVTC1-1</i> impairs the tolerance of rice seedlings to salt stress.

<p>(A), phenotypes of <i>OsVTC1-1</i> RI lines under salt stress. Control indicates that rice seedlings were grown under normal conditions, and NaCl indicates that seedlings were treated with 150 mM NaCl aqueous solution. (B), the percentage survival rates (Percentage is the ratio of number of plants with green new leaves to number of total plants) of <i>OsVTC1-1</i> RI plants after salt treatment in (A). WT represents ZH17 rice variety; RI1-1, RI1-2 and RI1-3 indicate independent RNA interference lines of <i>OsVTC1-1</i> in ZH17 background, respectively. About 50~60 seedlings were uses in each experiment. The bars represent SE (±) of three independent assays, and the asterisk indicates results significantly different from WT (**P<0.01 and *P<0.05). Significance was evaluated using the <i>t</i>-test.</p

<i>OsVTC1-1</i> RI lines show reduced grain production under salt stress.

<p>(A), phenotypes of <i>OsVTC1-1</i> RI lines grown under salt stress at harvest stage. (B), panicle number of <i>OsVTC1-1</i> RI plants with or without salt treatment. (C), grain number of the panicle of <i>OsVTC1-1</i> RI plants with or without salt treatment. (D), production of the panicle of <i>OsVTC1-1</i> RI plants with or without salt treatment. Control indicates that plants were grown under normal conditions, and NaCl indicates that plants were treated with 100 mM NaCl. WT represents ZH17; RI1-1, RI1-2 and RI1-3 indicate different RI lines of <i>OsVTC1-1</i> in ZH17 background. About 40~50 plants were uses in each experiment. Bars represent SE (±) of three independent assays, and the asterisk indicates that the results were significantly different from WT (**P<0.01 and *P<0.05). Significance was evaluated using the <i>t</i>-test.</p