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

Living on the edge:quantifying the structure of a fragmented forest landscape in England

Forest ecosystems have been widely fragmented by human land use, inducing significant microclimatic and biological changes at the forest edge. If we are to rigorously assess the ecological impacts of habitat fragmentation, there is a need to effectively quantify the amount of edge habitat within a landscape, and to allow this to be modelled for individual species and processes. Edge effect may extend only a few metres or as far as several kilometres, depending on the species or process in question. Therefore, rather than attempting to quantify the amount of edge habitat by using a fixed, case-specific distance to distinguish between edge and core, the area of habitat within continuously-varying distances from the forest edge is of greater utility. We quantified the degree of fragmentation of forests in England, where forests cover 10 % of the land area. We calculated the distance from within the forest patches to the nearest edge (forest vs. non-forest) and other landscape indices, such as mean patch size, edge density and distance to the nearest neighbour. Of the total forest area, 37 % was within 30 m and 74 % within 100 m of the nearest edge. This highlights that, in fragmented landscapes, the habitats close to the edge form a considerable proportion of the total habitat area. We then show how these edge estimates can be combined with ecological response functions, to allow us to generate biologically meaningful estimates of the impacts of fragmentation at a landscape scale

Tracing seed to seedling transmission of the wheat blast pathogen Magnaporthe oryzae

Wheat blast caused by Magnaporthe oryzae pathotype Triticum (MoT), initially restricted to South America, is a global threat for wheat after spreading to Asia in 2016 by the introduction of contaminated seeds, raising the question about transmission of the pathogen from seeds to seedlings, a process so far not well understood. We therefore studied the relationship between seed infection and disease symptoms on seedlings and adult plants. To accomplish this objective, we inoculated spikes of wheat cv. Apogee with a transgenic isolate (MoT-DsRed, with the addition of being resistant to hygromycin). We identified MoT-DsRed in experiments using hygromycin resistance for selection or by observation of DsRed fluorescence. The seeds from infected plants looked either apparently healthy or shrivelled. To evaluate the transmission, two experimental designs were chosen (blotter test and greenhouse) and MoT-DsRed was recovered from both. This revealed that MoT is able to colonize wheat seedlings from infected seeds under the ground. The favourable conditions of temperature and humidity allowed a high recovery rate of MoT from wheat shoots when grown in artificial media. Around 42 days after germination of infected seeds, MoT-DsRed could not be reisolated, indicating that fungal progression, at this time point, did not proceed systemically/endophytically. We hypothesize that spike infection might occur via spore dispersal from infected leaves rather than within the plant. Because MoT-DsRed was not only successfully reisolated from seed coats and germinating seeds with symptoms, but also from apparently healthy seeds, urgent attention is needed to minimize the risks of inadvertent dispersal of inoculum.Fil: Martinez, Sergio Ivan. Universidad Nacional de La Plata. Facultad de Ciencias Agrarias y Forestales. Departamento de Ciencias Biológicas. Centro de Investigaciones de Fitopatología. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigaciones de Fitopatología; ArgentinaFil: Wegner, Alex. Rwth Aachen University; AlemaniaFil: Bohnert, Stefan. Rwth Aachen University; AlemaniaFil: Schaffrath, Ulrich. Rwth Aachen University; AlemaniaFil: Perello, Analia Edith. Universidad Nacional de La Plata. Facultad de Ciencias Agrarias y Forestales. Departamento de Ciencias Biológicas. Centro de Investigaciones de Fitopatología. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigaciones de Fitopatología; Argentin

Potential for re-emergence of wheat stem rust in the United Kingdom.

Wheat stem rust, a devastating disease of wheat and barley caused by the fungal pathogenPuccinia graminis f. sp. tritici, was largely eradicated in Western Europe during the mid-to-latetwentieth century. However, isolated outbreaks have occurred in recent years. Here weinvestigate whether a lack of resistance in modern European varieties, increased presence of itsalternate host barberry and changes in climatic conditions could be facilitating its resurgence.We report the first wheat stem rust occurrence in the United Kingdom in nearly 60 years,with only 20% of UK wheat varieties resistant to this strain. Climate changes over the past 25years also suggest increasingly conducive conditions for infection. Furthermore, we documentthe first occurrence in decades of P. graminis on barberry in the UK . Our data illustrate thatwheat stem rust does occur in the UK and, when climatic conditions are conducive, couldseverely harm wheat and barley production