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

Inhibitory effect of liposomal quercetin on acute hepatitis and hepatic fibrosis induced by concanavalin A

Immune response plays an important role in the development of hepatic fibrosis. In the present study, we investigated the effects of quercetin on hepatitis and hepatic fibrosis induced by immunological mechanism. In the acute hepatitis model, quercetin (2.5 mg/kg) was injected iv into mice 30 min after concanavalin A (Con A) challenge. Mice were sacrificed 4 or 24 h after Con A injection, and aminotransferase tests and histopathological sections were performed. Treatment with quercetin significantly decreased the levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST). Consistent with this observation, treatment with quercetin markedly attenuated the pathologic changes in the liver. A hepatic fibrosis model was also generated in mice by Con A challenge once a week for 6 consecutive weeks. Mice in the experimental group were treated with daily iv injections of quercetin (0.5 mg/kg). Histopathological analyses revealed that treatment with quercetin markedly decreased collagen deposition, pseudolobuli development, and hepatic stellate cells activation. We also examined the effects of quercetin on the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and transforming growth factor beta (TGF-β) pathways by immunohistochemistry and real-time reverse transcriptase-polymerase chain reaction (RT-PCR). NF-κB and TGF-β production was decreased after treatment with quercetin, indicating that the antifibrotic effect of quercetin is associated with its ability to modulate NF-κB and TGF-β production. These results suggest that quercetin may be an effective therapeutic strategy in the treatment of patients with liver damage and fibrosis

Experiments of continuously and stably flowing lithium limiter in EAST towards a solution for the power exhaust of future fusion devices

Liquid lithium (Li) can partly ameliorate lifetime and power-exhaust issues of plasma facing components (PFCs) by enabling a self-healing, self-replenishing surface with a reduced susceptibility to neutron damage in future fusion devices. To assess operational stability and heat-exhaust capability under tokamak exposure, two generations of continuously flowing liquid Li (FLiLi) limiters on the concept of a thin flowing Li film have been successfully designed and tested in high performance discharges in EAST. The design uses a circulating Li layer with a thickness of <0.1 mm and a flow rate ∼2 cm3s−1. In addition, the limiter employs a novel electro-magnetic pump to drive liquid Li flow from a collector at the bottom of the limiter into a distributor at its top. Free surface gravitational flow closes the loop for a continuously flowing liquid Li film on the wetted PFC. Here we summarize key FLiLi limiter development and experimental results in H-mode plasmas. Keywords: Limiter, Lithium, Plasma facing component, EAS

Injected mass deposition thresholds for lithium granule instigated triggering of edge localized modes on EAST

The ability of an injected lithium granule to promptly trigger an edge localized mode (ELM) has been established in multiple experiments. By horizontally injecting granules ranging in diameter from 200 microns to 1mm in diameter into the low field side of EAST H-mode discharges we have determined that granules with diameter > 600 microns are successful in triggering ELMs more than 95% of the time. It was also demonstrated that below 600 microns the triggering efficiency decreased roughly with granule size. Granules were radially injected from the outer midplane with velocities ~ 80 m/s into EAST upper single null discharges with an ITER like tungsten monoblock divertor. These granules were individually tracked throughout their injection cycle in order to determine their efficacy at triggering an ELM. For those granules of sufficient size, ELM triggering was a prompt response to granule injection. By simulating the granule injection with an experimentally benchmarked neutral gas shielding (NGS) model, the ablatant mass deposition required to promptly trigger an ELM is calculated and the fractional mass deposition is determined.readme, digital data file