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

Analyzing genotype-by-environment interaction using curvilinear regression

In the context of multi-environment trials, where a series of experiments is conducted across different environmental conditions, the analysis of the structure of genotype-by-environment interaction is an important topic. This paper presents a generalization of the joint regression analysis for the cases where the response (e.g. yield) is not linear across environments and can be written as a second (or higher) order polynomial or another non-linear function. After identifying the common form regression function for all genotypes, we propose a selection procedure based on the adaptation of two tests: (i) a test for parallelism of regression curves; and (ii) a test of coincidence for those regressions. When the hypothesis of parallelism is rejected, subgroups of genotypes where the responses are parallel (or coincident) should be identified. The use of the Scheffé multiple comparison method for regression coefficients in second-order polynomials allows to group the genotypes in two types of groups: one with upward-facing concavity (i.e. potential yield growth), and the other with downward-facing concavity (i.e. the yield approaches saturation). Theoretical results for genotype comparison and genotype selection are illustrated with an example of yield from a non-orthogonal series of experiments with winter rye (Secalecereale L.). We have deleted 10 % of that data at random to show that our meteorology is fully applicable to incomplete data sets, often observed in multi-environment trials

Anestesia por infusão contínua de propofol em cães pré-medicados com acepromazina e fentanil Anesthesia by continuous infusion of propofol in dogs premedicated with acepromazine and fentanyl

O propofol (2,6 diisopropilfenol) é um agente hipnótico de ultra curta duração que produz sedação e hipnose similar aos barbitúricos, sendo desprovido de ação analgésica. Quimicamente, é o único agente anestésico venoso que pode ser usado tanto na indução como na manutenção anestésica. O presente trabalho objetivou avaliar freqüência cardíaca, respiratória, oximetria, pressão arterial média, volume minuto e volume corrente em cães pré-medicados com acepromazina e fentanil e anestesiados por infusão contínua de propofol. Dez cães foram submetidos à medicação pré-anestésica com acepromazina (0,1mg.kg-1) e fentanil (0,01mg.kg-1), indução (3,16mg.kg-1) e manutenção anestésica com propofol em infusão contínua por noventa minutos, na velocidade de 0,4mg.kg-1.min-1. Os parâmetros foram mensurados imediatamente após a indução, 10, 20, 30, 60 e 90 minutos após; final da infusão e 30 minutos após o seu término. Os parâmetros foram analisados por análise de variância para valores repetidos e as médias foram analisadas pelo teste de Tuckey em nível de 5%. O protocolo utilizado não produziu variações estatisticamente significativas em nenhum dos parâmetros analisados. Um animal apresentou apnéia durante a indução. Embasado nesses resultados, verifica-se que o presente protocolo é seguro e eficaz para a realização de anestesia venosa em caninos.<br>Propofol (2,6 diisopropylphenol) is an ultra short duration hypnotic agent that produces sedation and hypnosis similar to barbituric agent, but lacks analgesic action. This is a chemically unique anesthetic agent that can be used for induction and anesthetic maintenance. The objective of this research was to evaluate the cardiac and respiratory rate, oximetry, mean arterial blood pressure and tidal volume and minute volume in dogs premedicated with acepromazine and fentanyl and anesthetized by continuous infusion by propofol. Ten dogs were submitted to anesthesia by continuous propofol infusion during ninety minutes. Using acepromazine (0.1mg.kg-1) and fentanyl (0.01mg.kg-1) as pre anesthetic drugs, anesthesia was induced using propofol (3.16mg.kg-1) and maintained by continuous infusion of propofol in a rate of 0.4mg.kg-1 .min-1. The parameters were measured immediately after induction, at 10, 20, 30, 60 and 90 minutes following induction; by the end of infusion and 30 minutes after the end of infusion. The parameters were analyzed by analysis of variance for repeated measures and the means were analyzed by the Tuckey test to 5% of significance. The protocol used had no statistical effect on the parameters analyzed. One animal showed apnea during the induction phase. The results obtained in this experiment suggest that this protocol might be safely and efficiently used for routine intravenous anesthesia in dogs

Adaptabilidade e estabilidade de genótipos precoces de cana‑de‑açúcar no Rio Grande do Sul

O objetivo deste trabalho foi avaliar a adaptabilidade e estabilidade de genótipos de cana‑de‑açúcar de maturação precoce, quanto à produtividade de colmos e de Brix, no Estado do Rio Grande do Sul. Quinze genótipos de maturação precoce foram avaliados nas safras 2009/2010 e 2010/2011, por meio da análise de efeitos principais aditivos e interações multiplicativas (AMMI). As interações genótipo x ambiente foram de alta significância e evidenciaram a alteração de posição na classificação dos genótipos de um ambiente para outro. Novos genótipos superaram, em produtividade e estabilidade, o genótipo‑padrão precoce RB855156, embora este ainda se destaque pela produtividade, estabilidade moderada e ampla adaptabilidade. O genótipo RB966928 destacou-se pela riqueza e produtividade de Brix, estabilidade moderada e ampla adaptabilidade. Salto do Jacuí, RS, é o ambiente mais indicado para testes preliminares de seleção de genótipos

Brazilian Flora 2020: Leveraging the power of a collaborative scientific network

International audienceThe shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiversity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxonomic impediment to biodiversity research and conservation planning. The taxonomic impediment and the biodiversity crisis are widely recognized, highlighting the urgent need for reliable taxonomic data. Over the past decade, numerous countries worldwide have devoted considerable effort to Target 1 of the Global Strategy for Plant Conservation (GSPC), which called for the preparation of a working list of all known plant species by 2010 and an online world Flora by 2020. Brazil is a megadiverse country, home to more of the world's known plant species than any other country. Despite that, Flora Brasiliensis, concluded in 1906, was the last comprehensive treatment of the Brazilian flora. The lack of accurate estimates of the number of species of algae, fungi, and plants occurring in Brazil contributes to the prevailing taxonomic impediment and delays progress towards the GSPC targets. Over the past 12 years, a legion of taxonomists motivated to meet Target 1 of the GSPC, worked together to gather and integrate knowledge on the algal, plant, and fungal diversity of Brazil. Overall, a team of about 980 taxonomists joined efforts in a highly collaborative project that used cybertaxonomy to prepare an updated Flora of Brazil, showing the power of scientific collaboration to reach ambitious goals. This paper presents an overview of the Brazilian Flora 2020 and provides taxonomic and spatial updates on the algae, fungi, and plants found in one of the world's most biodiverse countries. We further identify collection gaps and summarize future goals that extend beyond 2020. Our results show that Brazil is home to 46,975 native species of algae, fungi, and plants, of which 19,669 are endemic to the country. The data compiled to date suggests that the Atlantic Rainforest might be the most diverse Brazilian domain for all plant groups except gymnosperms, which are most diverse in the Amazon. However, scientific knowledge of Brazilian diversity is still unequally distributed, with the Atlantic Rainforest and the Cerrado being the most intensively sampled and studied biomes in the country. In times of “scientific reductionism”, with botanical and mycological sciences suffering pervasive depreciation in recent decades, the first online Flora of Brazil 2020 significantly enhanced the quality and quantity of taxonomic data available for algae, fungi, and plants from Brazil. This project also made all the information freely available online, providing a firm foundation for future research and for the management, conservation, and sustainable use of the Brazilian funga and flora