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

Quantitative and correlation analysis of the DNA methylation and expression of DAPK in breast cancer

Background Death-associated protein kinase 1 (DAPK) is an important tumor suppressor kinase involved in the regulation of multiple cellular activities such as apoptosis and autophagy. DNA methylation of DAPK gene was found in various types of cancers and often correlated with the clinicopathological characteristics. However, the mRNA and protein expression of DAPK in the same sample was rarely measured. Thus, it was unclear if the correlation between DAPK gene methylation and clinicopathological parameters was due to the loss of DAPK expression. Methods In this study, the DNA methylation rate, mRNA and protein expression of DAPK was quantitatively detected in 15 pairs of breast cancer patient samples including tumor (T) and adjacent non-tumor (N) tissues. Results The correlation between DNA methylation rate and mRNA expression, together with the correlation between mRNA and protein expression, was calculated. No correlation was observed between any levels using either the measurement value of each sample or the T/N ratio of each pair. Discussion These data suggested that the DNA methylation status of DAPK did not correlate well with its mRNA or protein expression. Extra caution is needed when interpreting the DNA methylation data of DAPK gene in clinical studies

Quantitative and correlation analysis of the DNA methylation and expression of DAPK in breast cancer

Background Death-associated protein kinase 1 (DAPK) is an important tumor suppressor kinase involved in the regulation of multiple cellular activities such as apoptosis and autophagy. DNA methylation of DAPK gene was found in various types of cancers and often correlated with the clinicopathological characteristics. However, the mRNA and protein expression of DAPK in the same sample was rarely measured. Thus, it was unclear if the correlation between DAPK gene methylation and clinicopathological parameters was due to the loss of DAPK expression. Methods In this study, the DNA methylation rate, mRNA and protein expression of DAPK was quantitatively detected in 15 pairs of breast cancer patient samples including tumor (T) and adjacent non-tumor (N) tissues. Results The correlation between DNA methylation rate and mRNA expression, together with the correlation between mRNA and protein expression, was calculated. No correlation was observed between any levels using either the measurement value of each sample or the T/N ratio of each pair. Discussion These data suggested that the DNA methylation status of DAPK did not correlate well with its mRNA or protein expression. Extra caution is needed when interpreting the DNA methylation data of DAPK gene in clinical studies

Short Placental Telomere was Associated with Cadmium Pollution in an Electronic Waste Recycling Town in China

<div><p>In Guiyu, an electronic waste recycling site near Shantou, Guangdong province, China, primitive ways of e-waste processing have caused severe cadmium and lead pollution to the local residents. However, the possible effects of cadmium or lead pollution to genomic integrity of the local residents have not been investigated. We examined the possible relationship between cadmium and lead concentrations in placenta and placental telomere length in Guiyu and compared the data with that of a non-polluted town. Graphite furnace atomic absorption spectrometry and real-time PCR were used to determine placental cadmium and lead concentrations, and placental telomere length. We found that placental cadmium concentration was negatively correlated with placental telomere length (r = −0.138, p = 0.013). We also found that placental cadmium concentration of 0.0294 µg/g might be a critical point at which attrition of placental telomere commenced. No significant correlation between placental lead concentration and placental telomere length was detected (r = 0.027, p = 0.639). Our data suggest that exposure to cadmium pollution during pregnancy may be a risk factor for shortened placental telomere length that is known to be related to cancer development and aging. Furthermore, grave consequence on the offspring from pregnancies in e-waste polluted area is indicated.</p> </div

Exploration of influencing factors for placental telomere length based on unconditional logistic regression analysis.

<p>a: long or short placental telomere length, taking the mean of placental telomere length of the control group as the cutting point, *: p<0.01.</p

Correlation of T/S ratio and the mean terminal restriction fragment (TRF) length.

<p>(A) Correlation of T/S ratio assessed by real-time PCR-based telomere assay and the mean TRF length determined by southern blotting in ten DNA samples. The linear regression line that best fit the data (p = 0.002) is shown. (B) The mean terminal restriction fragment (TRF) length was assessed by southern blotting. Size of molecular weight markers (Kb) is shown at the left side. S₁–S₉: nine randomly-selected DNA samples, Ref: the reference DNA used in real-time PCR-based telomere assay.</p

Spearman correlation analysis of placental cadmium concentration and placental lead concentration with placental telomere length.

*<p>: p<0.05.</p