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

Morphological variation in an early developmental stage (glass eel) of European eel (Anguilla anguilla)

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Non-algae scraping vs algae scraping, comparison between Synodontis and Atopochilus (Siluriformes: Mochokidae)

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Searching the onset of head shape bimodality in European eels (Anguilla anguilla)

The life cycle of the European eel (Anguilla anguilla) remained a mystery until the 20th century, when Schmidt discovered that the Sargasso Sea was its spawning area. However, many aspects of the eel’s life cycle remain poorly understood. Among these is the bimodal distribution in head shape, with broad- and narrowheaded phenotypes reported in the yellow eel stage. Although this has been linked to dietary preferences of the yellow eels, very little is known about why, how and when this dimorphism arises during their ontogeny. To find out whether this dimorphism indeed appears in relation to trophic niche segregation, we examined head shape variation at an earlier ontogenetic stage, the glass eel stage, as at this stage, eels are considered to be non-feeding. Head shape was studied in glass eels captured from the Yser river mouth (N=275), the Leopold Canal (N=112; Belgium) and from the rivers Severn, Trent and Parret (N=153; U.K.) by both taking measurements (head width/head length) and using an outline analysis. Our results show that there’s already considerable variation in broadness and bluntness of the head at the glass eel stage, but no unambiguous support for head shape dimorphism was found. However, as variation in head width/head length ratios in non-feeding glass eels shows a similar range as in feeding yellow eels, head shape in European eel might be at least partially determined through other mechanisms than trophic segregation

The search for the onset of head shape bimodality in European eel (Anguilla anguilla)

The life cycle of the European eel (Anguilla anguilla) remained a mystery until the 20th century, when Schmidt discovered that the Sargasso Sea was its spawning area. However, many aspects of the eel’s life cycle remain poorly understood. Among these is the bimodal distribution in head shape, with broad- and narrowheaded phenotypes reported in the yellow eel stage. Although this has been linked to dietary preferences of the yellow eels, very little is known about why, how and when this dimorphism arises during their ontogeny. To find out whether this dimorphism indeed appears in relation to trophic niche segregation, we examined head shape variation at an earlier ontogenetic stage, the glass eel stage, as at this stage, eels are considered to be non-feeding. Head shape was studied in glass eels from the Yser river mouth, the Leopold Canal and from the rivers Severn, Trent and Parret by both taking measurements (head width/head length) and using an outline analysis. Our results show that there’s already considerable variation in broadness and bluntness of the head at the glass eel stage, but no unambiguous support for head shape dimorphism was found. However, as variation in head width/head length ratios in non-feeding glass eels shows a similar range as in feeding yellow eels, head shape in European eel might be at least partially determined through other mechanisms than trophic segregation