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

Evaluation of bacterial contamination on three different surfaces within domestic refrigerators

The objectives of this study were to analyze the number of microorganisms, fungal composition and the correlation between bacterial enrichment and air quality on three internal surfaces (the inner wall, shelf, and basket) of domestic refrigerators. The results showed that the inner wall had a significantly lower number of coliforms (P < 0.05), and the range was 0.2−2.5 log MPN cm−2. The total bacterial counts and psychrophilic bacterial counts on three internal surfaces in the same refrigerator tended to be consistent. Moreover, the inner wall owned a simpler bacterial community structure. At the genus level of fungi, the dominant flora of both the inner wall and shelf were Saccharomyces spp. and Candida spp., while Saccharomyces spp., Candida spp. and Fistulina spp. took superiority in the basket. Specifically, Shannon index and Simpson index, which represent the bacterial community diversity, were the lowest on the wall, and six bacterial species on the inner wall had relative abundance higher than 0.5% of the total operational taxonomic units (OTUs), while for the shelf and basket, there were 12 and 11 bacterial species respectively. Also, there was a significant negative correlation in the basket between the chao1 index and PM2.5. This study could provide guidance for the sanitation and recommend adequate packaging of foods stored in refrigerators

Sleep disturbance and psychological distress are associated with functional dyspepsia based on Rome III criteria

Abstract Background Functional dyspepsia (FD) is considered a bio-psychosocial disorder. The role of psychosocial factors in FD pathogenesis remains unclear. Methods This study evaluated sleep quality and mood symptoms in patients with FD, assessing the associations of FD severity, disordered sleep, and psychological symptoms. One-hundred-and-fifteen adult patients with typical FD symptoms were enrolled alongside 61 healthy volunteers. Rome III criteria were used to evaluate FD symptoms; sleep disorder was assessed with the Pittsburgh Sleep Quality Index (PSQI), and Symptom Checklist-90-Revised (SCL-90R) was utilized to determine the status of depression, anxiety and other psychological symptoms. Results PSQI scores and nine symptomatic dimensions of SCL-90R were significantly higher in FD patients than in controls. Multiple logistic regression indicated that lower BMI, lower level of education, and sleep disturbance were independently associated with FD and FD subgroups. Hostility and phobic anxiety were independent risk factors for FD. Further analysis showed that hostility was an independent risk factor for both FD subgroups, and somatization and additional psychiatric symptoms for epigastric pain syndrome. Conclusions We found that FD was associated with sleep disorder and psychopathological factors. These findings suggest that implementing sleeping and/or psychological therapies may help reduce FD symptoms

Transcription Factor Sp1 Promotes the Expression of Porcine ROCK1 Gene

Rho-associated, coiled-coil containing protein kinase 1 (ROCK1) gene plays a crucial role in maintaining genomic stability, tumorigenesis and myogenesis. However, little is known about the regulatory elements governing the transcription of porcine ROCK1 gene. In the current study, the transcription start site (TSS) was identified by 5’-RACE, and was found to differ from the predicted one. The region in ROCK1 promoter which is critical for promoter activity was investigated via progressive deletions. Site-directed mutagenesis indicated that the region from −604 to −554 bp contains responsive elements for Sp1. Subsequent experiments showed that ROCK1 promoter activity is enhanced by Sp1 in a dose-dependent manner, whereas treatment with specific siRNA repressed ROCK1 promoter activity. Electrophoretic mobility shift assay (EMSA), DNA pull down and chromatin immunoprecipitation (ChIP) assays revealed Sp1 can bind to this region. qRT-PCR and Western blotting research followed by overexpression or inhibition of Sp1 indicate that Sp1 can affect endogenous ROCK1 expression at both mRNA and protein levels. Overexpression of Sp1 can promote the expression of myogenic differentiation 1(MyoD), myogenin (MyoG), myosin heavy chain (MyHC). Taken together, we conclude that Sp1 positively regulates ROCK1 transcription by directly binding to the ROCK1 promoter region (from −604 to −532 bp) and may affect the process of myogenesis

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 science. © The Author(s) 2019. Published by Oxford University Press