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

Local Resistance in Early Medieval Chinese Historiography and the Problem of Religious Overinterpretation

Official Chinese historiography is a treasure trove of information on local resistance to the centralised empire in early medieval China (third to sixth century). Sinologists specialised in the study of Chinese religions commonly reconstruct the religious history of the era by interpreting some of these data. In the process, however, the primary purpose of the historiography of local resistance is often overlooked, and historical interpretation easily becomes ‘overinterpretation’—that is, ‘fabricating false intensity’ and ‘seeing intensity everywhere’, as French historian Paul Veyne proposed to define the term. Focusing on a cluster of historical anecdotes collected in the standard histories of the four centuries under consideration, this study discusses the supposedly ‘religious’ nature of some of the data they contain

Immunoblot analysis of ApoE oxidized by VPO1.

<p>A. VLDL was oxidized by MPO or VPO1 as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057571#s2" target="_blank">Materials and Methods</a>. The oxidized lipoproteins were separated by SDS-PAGE and transferred to PVDF membrane. The blot was analyzed by using anti-ApoE antibody and visualized using chemiluminescence. B. The same as in A, but the samples were separated by using native PAGE. C. rApoE was oxidized by VPO1 or reagent HOCl. Blot was analyzed as in A.</p

Effect of ox-ApoE on the transportation of plasma triglycerides and cholesterol.

<p>A. Changes of plasma triglycerides by administration of native and ox-ApoE. B. Changes of plasma cholesterol by administration of native and ox-ApoE. Plasma triglyceride and cholesterol concentrations were measured 1 hr before and after of ApoE administration. *p<0.05 <i>vs</i>. native ApoE. **p<0.05 <i>vs</i>. native ApoE (paired t-test). n = 5.</p

Loss of free amino groups and tryptophan residues in oxidized ApoE.

<p>A. Loss of free amino groups in oxidized ApoE. ApoE was oxidized by VPO1/H₂O₂/Cl⁻, MPO/H₂O₂/Cl⁻, or HOCl for 3 hrs at 37°C (n = 3). Unmodified amino groups were quantified with the method using trinitrobenzene sulfonic acid as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057571#s2" target="_blank">Materials and Methods</a>. Absorbance was measured at 340 nm. B. Loss of tryptophan residues following ApoE oxidation. ApoE was incubated with VPO1/H₂O₂/Cl⁻, MPO/H₂O₂/Cl⁻ or HOCl for 3 hrs at 37°C (n = 3) as in A. Fluorescence from free tryptophan residue (emission 335 nm/excitation 280 nm) was quantified with a BioTek Microplate Reader. Trp: tryptophan. Data are shown as means ± SEM; *p<0.05 <i>vs</i>. native ApoE; n = 3.</p

Ox-ApoE binds weakly to emulsion particles.

<p>A. Ox-ApoE binding with triglyceride-PC emulsion particles. Native and ox-ApoE were incubated with triglyceride-PC emulsion particles at room temperature for 1 hr with gentle shaking. Emulsion particles and lipid-free buffer were segregated by centrifugation. Equal amount of samples from top and lower layers (contain lipid-bound ApoE and free ApoE, respectively) were carried out for Western blot analysis using anti-ApoE antibody. B. Ox-ApoE binding with PC emulsion particles. Native and ox-ApoE were incubated with PC emulsion particles at room temperature for 1 hr with gentle shaking. Emulsion particles and lipid-free buffer were segregated by centrifugation as in A. Equal amount of samples from top and lower layers (contain lipid-bound ApoE and free ApoE, respectively) were carried out for Western blot analysis using anti-ApoE antibody. C. Quantification of ApoE and ox-ApoE binding to triglycerides-PC emulsion particles from data in A. The ratio was calculated as emulsion particle-bound ApoE/free ApoE. D. Quantification of ApoE and ox-ApoE binding to PC emulsion particles from data in B. The ratio was calculated as emulsion particle-bound ApoE/free ApoE. Data are shown as means ± SEM; *p<0.05. n = 3.</p

Effect of ox-ApoE on triglyceride, cholesterol and PC efflux from foam cells.

<p>A. Cellular triglyceride efflux by native and ox-ApoE. B. Cellular cholesterol efflux by native and ox-ApoE. C. Cellular PC efflux by native and ox-ApoE. D. Detection of triglycerides in supernatant. E. Detection of cholesterol in supernatant. F. Detection of PC in supernatant. THP-1 cells were loaded with lipids as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057571#s2" target="_blank">Materials and Methods</a>. Efflux of triglycerides, cholesterol, and PC was initiated by addition of native or ox-ApoE in cultured foam cells. After treatment of 9 hrs, triglycerides, cholesterol, and PC in supernatant were measured by the respect kit. After treatment of 24 hrs, the cellular triglycerides, cholesterol, and PC were measured with the respect kit. Tg: triglycerides; Ch: cholesterol; PC: phosphatidylcholine. Data are shown as means ± SEM; *p<0.05 vs. PBS group. n = 3.</p

Localization of VPO1 and ApoE in atherosclerotic lesion.

<p>Immunofluorescence staining was carried out for detection of ApoE (A) and VPO1 (B) using sections from mouse atherosclerotic lesions. C. Merged image of A and B. D. Nuclei were visualized with Hoechst staining (blue). E. Bright-field image. F. Merged image of A, B, D, and E. Scale bar, 20 µm. Magnification: x400.</p