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

Characterization of Salmonella enterica serovars recovered from meat products legally and illegally imported into the EU reveals the presence of multiresistant and AmpC-producing isolates

Abstract Background Food products of animal origin brought into the EU from third countries, both legally and illegally, can harbor foodborne pathogens such as Salmonella enterica. In this study, we examined five S. enterica isolates recovered either from legally imported chicken meat (n = 3) or from meat products confiscated from air travel passengers arriving in Germany (n = 2). The isolates were serotyped and further characterized by antimicrobial susceptibility testing, PCR-detection and sequencing of genes associated with antimicrobial resistances, and macrorestriction analysis. Transferability of resistance to third-generation cephalosporins was assessed by conjugation experiments and the plasmids tested for their incompatibility groups. Results The three isolates from legal imports were identified as S. Heidelberg or as non-flagellated. All three isolates were identified as AmpC producers carrying bla CMY-2 and as non-susceptible to ciprofloxacin. They were additionally resistant to tetracycline and sulfamethoxazole. The bla CMY-2-carrying plasmids were transferable by conjugation and belonged to incompatibility groups IncI1 or IncA/C. The two isolates from illegally imported meat belonged to the serovars Infantis or Weltevreden. The former was phenotypically resistant to five classes of antimicrobial agents while the S. Weltevreden isolate was fully susceptible to all agents tested. Conclusion The results of this study demonstrate that meat products imported from third countries, both legally and illegally, can harbor multiresistant Salmonella enterica. Consequently, these imports could constitute a source for the dissemination of antimicrobial resistant isolates, including those resistant to third-generation cephalosporins and fluoroquinolones

The quantity and quality of illegally imported products of animal origin in personal consignments into the European Union seized at two German airports between 2010 and 2014

The import of products of animal origin (POAO) in travellers' personal consignments presents a considerable risk of introducing animal diseases and emerging zoonoses into the European Union. The current regulation (EU) 206/2009 implements strict measures for illegally imported POAO, whereupon non-complying products have to be seized and destroyed regardless. Especially airports serve as global bottlenecks for illegally imported POAO where passenger controls of non-European flights are performed by customs and veterinary services in collaboration. Results of these control measures have to be submitted in the form of annual reports to the European Commission. However, few data on qualities and quantities of seizures have been published so far. In this study, POAO seized at two German airports between 2010 and 2014 were analysed in terms of quantities, qualitative categories and region of origin. In most years considered, more than 20 tonnes POAO were seized at each airport. However, reported amounts of seizures seem to be only the tip of the iceberg as an all-passenger control is not feasible and therefore travellers are only spot-checked. The analysis suggests that the organisational structures of both customs and official veterinary services and their different risk perceptions interfere in completing an effective ban on the illegal import of POAO

Total passengers, total seizures, seizures/day, seizure-passenger ratio and mean seized amount in kilogrammes per passenger at IA 1 and IA 2, 2010–2014.

<p>Total passengers, total seizures, seizures/day, seizure-passenger ratio and mean seized amount in kilogrammes per passenger at IA 1 and IA 2, 2010–2014.</p

Other POAO (in kg) seized at IA 1 according to region of origin between 2010–2014.

<p>Other POAO (in kg) seized at IA 1 according to region of origin between 2010–2014.</p

Total amount of seized POAO (in kg) and mean amount of kilogrammes per passenger at IA 1, 2010–2014.

<p>Total amount of seized POAO (in kg) and mean amount of kilogrammes per passenger at IA 1, 2010–2014.</p