Changes in the geographical distribution of plant species and climatic variables on the West Cornwall peninsula (South West UK)

Recent climate change has had a major impact on biodiversity and has altered the geographical distribution of vascular plant species. This trend is visible globally; however, more local and regional scale research is needed to improve understanding of the patterns of change and to develop appropriate conservation strategies that can minimise cultural, health, and economic losses at finer scales. Here we describe a method to manually geo-reference botanical records from a historical herbarium to track changes in the geographical distributions of plant species in West Cornwall (South West England) using both historical (pre-1900) and contemporary (post-1900) distribution records. We also assess the use of Ellenberg and climate indicator values as markers of responses to climate and environmental change. Using these techniques we detect a loss in 19 plant species, with 6 species losing more than 50% of their previous range. Statistical analysis showed that Ellenberg (light, moisture, nitrogen) and climate indicator values (mean January temperature, mean July temperature and mean precipitation) could be used as environmental change indicators. Significantly higher percentages of area lost were detected in species with lower January temperatures, July temperatures, light, and nitrogen values, as well as higher annual precipitation and moisture values. This study highlights the importance of historical records in examining the changes in plant species’ geographical distributions. We present a method for manual geo-referencing of such records, and demonstrate how using Ellenberg and climate indicator values as environmental and climate change indicators can contribute towards directing appropriate conservation strategies

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 antioxidant and antibacterial activities of the stems of Flammulina velutipes and Hypsizygus tessellatus (white and brown var.) extracted with different solvents

Mushrooms are rich in pharmacologically-important phytochemicals with reported medicinal values. In this study, the antibacterial activity of Flammulina velutipes (Enoki), Hypsizygus tessellatus (brown (Buna shimeji) and white (Bunapi shimeji) variants) stem extracts prepared with different solvents (water, methanol, acetone, and ethyl acetate) was investigated against Escherichia coli (E. coli ATCC 25922), Serratia marscenscens (S. marscenscens ATCC14756), Bacillus subtilis (B. subtilis ATCC 23857), and Staphylococcus aureus (S. aureus ATCC 25923). Their antioxidant activities were evaluated using radical scavenging assays of 1,1-diphenyl-2-picrylhydrazyl (DPPH), hydrogen peroxide (H2O2) and ferric reducing power (FRP). The water extracts of Enoki, Buna shimeji, and Bunapi shimeji showed bacterial growth inhibition in a concentration-dependent manner. From the obtained results, all the Enoki extracts showed a significant inhibition of the gram positive bacterial species (E. coli and S. marcescens > 68%) and a reduced inhibition of the gram negative bacterial species (B. subtilis and S. aureus < 45%, p < 0.05) after 24 h of incubation, while water extracts of Buna shimeji showed a significantly lower bacterial growth inhibition (< 60%) against all the studied bacteria. Bunapi shimeji extract inhibited S. marscenscens, E. coli, B. subtilis, and S. aureus by 54, 67, 46, and 44%, respectively. Methanol, acetone and ethyl acetate extracts showed significantly lower antibacterial activities (p < 0.05) compared to water extracts. Similarly, water extracts of Enoki, Bunapi shimeji and Buna shimeji showed significant antioxidant activities using DPPH (67.37 ± 0.01, 66.30 ± 0.18 and 42.44 ± 0.18%, respectively), hydrogen peroxide (67.87 ± 0.000, 45.52 ± 0.160 and 52.08 ± 0.000% respectively), and FRP (0.891 ± 0.001, 0.413 ± 0.001 and 0.491 ± 0.001, respectively) at the concentration of 1 mg/mL, compared to their respective methanol, acetone and ethyl acetate fractions. Upon LC-MS analysis of the most potent fraction (Enoki water extract), several phenolic compounds were identified, of which chromogenic acid, Methyl-5-O-caffeoylquinate, Kukoamine A, Kushenol K, Methyl Kushenol C, Glabrol, Sanggenon J, Corylin, and Moracenin C were confirmed. The antioxidant activities of the water extracts of Enoki, Buna shimeji and Bunapi shimeji correlated with their total phenolic and flavonoid contents, which were (166.56 ± 1.50, 108.13 ± 0.32 and 116.71 ± 0.01 µg gallic acid equivalent (GAE)/mg, respectively) and (96.33 ± 0.03, 82.18 ± 0.20 and 91.37 ± 0.15 µg quercetin equivalent (QE)/mg, respectively). Collectively, the study results have shown the studied mushrooms as potential natural sources of pharmacological agent

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