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

BF₃‑Promoted Ring Expansion of Iminylphosphiranes and Acylphosphiranes for Divergent Access to 1,2-Azaphospholidines and 1,2-Dihydrophosphetes

Ring expansion of strained small rings provides an efficient method for the synthesis of various high-value carbocycles and heterocycles. Here we report BF3·Et2O as both an activating reagent and fluorine source, enabling ring expansion of phosphirane and P–F bond formation. Treatment of 1-iminylphosphirane complexes with BF3·Et2O resulted in 1,2-azaphospholidines, while the reaction of 1-acylphosphirane complexes with BF3·Et2O afforded 1,2-dihydrophosphetes. The reaction path was tuned by the nucleophilicity of the N and O atoms toward the intermediate phosphenium cation

Micrographs of nHA-CS.

<p>The nHA-CS scaffold exhibited a three-dimensional porous structure in which the nHA particles were evenly distributed throughout the pore surface (figure magnification 500×).</p

CT evaluation of the implants.

<p><b>(A)</b> Representative CT images of the implants scanned at 2, 4, 6, 8, and 12 weeks post-implantation. Red arrows indicate the implants. <b>(B)</b> The CT values of the implants in the nHA-CS+cells group were significantly greater than those of the nHA-CS group (*<i>P</i> < 0.05), indicating that <i>de novo</i> bone formation was greater in the nHA-CS+cells group.</p

BMSCs and identification of osteogenic differentiation at passage 3.

<p><b>(A)</b> BMSCs cultured in basic medium exhibited typical elongated fibroblast-like morphology. <b>(B)</b> ALP expression was identified by calcium-cobalt staining of black particle deposition in cells after one week of osteogenic induction. <b>(C)</b> Calcified nodules that formed in the extracellular matrix were detected by Alizarin red staining after three weeks of osteogenic induction. The red arrow indicates a calcified nodule (figure magnification 100×).</p

Histological examination of Masson's trichrome staining.

<p><b>(A)</b> Representative Masson's trichrome staining images showing the expression of collagen in the two groups at different time points (figure magnification 100×). <b>(B)</b> The analysis of the proportions of the collagen area indicate that significantly more collagen was present in the nHA-CS+cells group than the nHA-CS group (*<i>P</i> < 0.05), indicating that the nHA-CS+cells group formed more <i>de novo</i> bone than the nHA-CS+cells group.</p

The detailed osteogenic medium component list.

<p>The detailed osteogenic medium component list.</p

Histological examination of HE staining.

<p><b>(A)</b> Representative HE images of implants from the two groups harvested at different time points (figure magnification 100×). <b>(B)</b> The analysis of the proportions of newly formed bone area indicated that the nHA-CS+cells group gained greater amounts of <i>de novo</i> bone compared with the nHA-CS group (*<i>P</i> < 0.05). <b>(C)</b> The analysis of the proportions of the scaffold area revealed that the nHA-CS+cells group exhibited significant scaffold degradation than the nHA-CS group (*<i>P</i> < 0.05).</p

Fluorescent image of DAPI-labeled cells on pore surfaces of scaffolds.

<p>BMSCs adhered in the vicinity of the pores and its edges of a nHA-CS scaffold. Red arrows indicate labeled cells (figure magnification 100×).</p