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

Isolamento e identificação de fungos micorrízicos rizoctonióides associados a três espécies de orquídeas epífitas neotropicais no Brasil Isolation and identification of rhizoctonia-like mycorrhizal fungi associated to three neotropical epiphytic orchid species in Brazil

Distúrbios causados pelo homem têm resultado no aumento do risco de extinção de diversos táxons de orquídeas nativas da Mata Atlântica no Brasil. Na natureza, orquídeas utilizam obrigatoriamente fungos endomicorrízicos para a germinação de sementes e desenvolvimento da plântula, ao menos nos primeiros estádios do seu ciclo de vida. Assim, fungos micorrízicos associados ao sistema radicular de orquídeas nativas vêm sendo isolados, caracterizados e armazenados para uso em futuros programas de conservação de espécies de orquídeas, por meio da germinação simbiótica. Três isolados de fungos micorrízicos rizoctonióides foram obtidos do sistema radicular de três espécies de orquídeas neotropicais, Gomesa crispa, Campylocentrum organense e Bulbophyllum sp., de três diferentes fragmentos de Mata Atlântica no Brasil. Estudos taxonômicos, baseados na condição nuclear, morfologia da hifa vegetativa e ultra-estrutura do septo dolipórico, revelaram que os isolados pertencem aos gêneros Ceratorhiza e Rhizoctonia. Esse é o primeiro relato do isolamento de fungos micorrízicos associados ao sistema radicular dessas espécies de orquídeas neotropicais. Aspectos relativos à taxonomia e ao uso desses isolados no contexto de um programa de conservação de orquídeas nativas são discutidos.<br>Anthropogenic disturbances have resulted in an increased threat of extinction of many native orchid taxa in Brazil's Atlantic rain forest. In nature, orchids utilize mycorrhizal fungi to initiate seed germination and seedling development, at least in the early stages of their life cycle. Mycorrhizal fungi associated with the roots of orchids have thus been isolated, characterized and stored as important resources for a future conservation program of orchid species through symbiotic seed germination. Three mycorrhizal Rhizoctonia-like fungi were isolated from roots of three neotropical orchid species Gomesa crispa, Campylocentrum organense and Bulbophyllum sp. from three different Atlantic rain forest fragments in Brazil. Taxonomic studies based on the nuclear condition, vegetative hyphal morphology and septal pore ultrastructure revealed that the isolates belong to the genera Ceratorhiza and Rhizoctonia. This is the first report on the isolation of mycorrhizal fungal species associated to the referred neotropical orchid species. Aspects concerning their taxonomy and use in the context of a native orchid conservation programs are discussed

Targeting either GH or IGF-I during somatostatin analogue treatment in patients with acromegaly:A randomized multicentre study

Context Discordant GH and IGF-I values are frequent in acromegaly. The clinical significance and its dependence on treatment modality and of glucose-suppressed GH (GHnadir) measurements remain uncertain. Objective To evaluate the effects of targeting either IGF-I or GH during somatostatin analogue (SA) treatment. Patients and Methods 84 patients with controlled acromegaly after surgery (n = 23) or SA (n = 61) underwent a GH profile including an OGTT, at baseline and after 12 months. SA patients were randomized to monitoring according to either IGF-I (n = 33) or GHnadir (n = 28). SA dose escalation was allowed at baseline and 6 months. Main outcome measures GHnadir and IGF-I at baseline and 12 months, and disease-specific Quality of Life (QoL). Results IGF-I and fasting GH levels were comparable between the surgery and the SA group, whereas GHnadir (µg/L) was lower in the surgery group (GHnadir 0.7 ± 0.1 vs 0.3 ± 0.1, P &lt; 0.01). SA dose increase was performed in 20 patients in the GH group and in 8 patients in the IGF-I group (P = 0.02), which increased the number of concordantly controlled patients (P = 0.01). QoL was only mildly affected at baseline in all groups and did not changed consistently during the study. Conclusion (1) Discordant values in terms of high GH levels are prevalent in SA patients and more so if applying glucose-suppressed GHnadir; (2) targeting discordant levels of either GH or IGF-I translates into SA dose increase and improved biochemical control; (3) even though QoL was not improved in this study, we suggest biochemical assessment of disease activity to include glucose-suppressed GHnadir also in SA patients. </jats:sec