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

Mapping the global dimensions of US wildlife imports

Wildlife trade remains a major driver of accelerating global biodiversity loss, yet our knowledge of this trade remains fragmented. Our understanding of trade origins and flows is particularly poor, which prevents decision makers from identifying trends or assessing law enforcement efficacy. We assess the global dimensions of trade into the US across multiple taxonomic groups over two decades. We analyze geographic patterns to identify the origins of traded wildlife, including in endemic and threatened species. We identify major inconsistencies in provenance of wild species exports, as many traded species are labeled “wild,” but not native to the country of export. The European Union represents a major source of arachnids and reptiles, many declared as wild. We further highlight a range of likely reporting errors, potential species laundering, and possible Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) violations. Counteracting biodiversity threats posed by the global wildlife trade requires better data, better standardization, and clear interventions to manage trade sustainably

Azospirillum Cell Aggregation, Attachment, and Plant Interaction

'Azospirillum' cellular and morphological transformation in culture as well as cyst formation, aggregation, and flocculation in response to nutritional limitations and increasing oxygen levels are discussed and typical protocols for flocculation and aggregation are presented. An overview of the mechanisms of attachment to plant roots and other surfaces is followed by protocols for labeling 'Azospirillum' cells with reporter genes and using such genetically labelled cells in qualitative and quantitative assays of 'Azospirillum'-plant associations. The potential of 'Azospirillum' in plant pathogen and disease suppression is discussed