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

Escala diagramática para avaliação de mofo cinzento (Amphobotrys ricini) da mamoneira (Ricinus communis L.) Diagramatic scale to assess gray mold (Amphobotyrs ricini) in castor bean (Ricinus communis L.)

O objetivo do trabalho foi a elaboração de uma escala diagramática para avaliação de mofo cinzento causado por Amphobotrys ricini (Buchw.) em mamoneira (Ricinus communis L.). Utilizaram 59 cachos, que foram desinfestados em solução de hipoclorito de sódio a 2% por 30 segundos e em água destilada e esterilizada. Depois foram acondicionados em bandejas com espuma umedecida, onde receberam discos de micélio de 5mm do patógeno, permanecendo em câmara climática a 25ºC e UR de 80%. Observou-se a evolução da doença e foram obtidos fotos dos cachos doentes diariamente. Para a determinação da porcentagem de severidade dos cachos, os frutos infectados e sadios foram contados, estimando-se dessa forma a porcentagem da área lesionada e elaborando uma escala diagramática com seis níveis de severidade. A adoção da escala proposta, melhorou a acurácia (R²=0,94), com valores de "a" não significativamente diferentes de zero (0) e os valores de "b" não diferentes de um (1).<br>The aim of the present study was to develop a diagrammatic scale to assess gray mold caused by Amphobotrys ricini in castor bean (Ricinus communis L.). The experiment included 59 clusters, which were disinfected in solution of sodium hypochlorite to 2% for 30 seconds and distilled water and sterilized. Then, they were packed in moistened foam trays which received 5mm mycelial discs, and were kept in a climatic chamber at 25º C and 80%. RH. The disease evolution was observed daily pictures of the clusters diseased. To determine the severity percentage of the bunches, infected and healthy fruits were counted, estimating thus the percentage of the injured area, and developing a diagrammatic scale with six severity levels. The adoption of the proposed scale, improved the accuracy (R² = 0,94) "a" values were not significantly different from zero (0) and "b" values were not significantly different from one (1)

Potential of biogas and methane production from anaerobic digestion of poultry slaughterhouse effluent

The objective of this study was to evaluate the efficiency of anaerobic digestion on the treatment of effluent from poultry slaughterhouse. The experiment was conducted at the Laboratory of Waste Recycling from Animal Production/FCA/UFGD. During four weeks, eight experimental digesters, semi-continuous models, were loaded and set according to the hydraulic retention time (HRT) of 7, 14, 21 and 28 days, and according to the solid fraction treatment, separated with 1 mm sieve or without separation. The average weekly production of biogas and methane as well as the methane concentrations, the potential production per amount of chemical oxygen demand (COD) added and reduced, the concentrations of N, P and K at the beginning and end of process, and the most likely numbers of total and thermotolerant coliforms were evaluated. For data analysis, a completely randomized design was performed in a 4 × 2 factorial arrangement (4 HRT: 7, 14, 21 and 28 days and separation with 1 mm sieve or without separation), with repetition over time. The highest production of biogas and methane was statistically significant for the HRT of 7 and 14 days (5.29 and 2.38 L of biogas and 4.28 and 1.73 L of methane, respectively). There was an interaction between HRT and the separation of the solid with sieve and the highest production was obtained in the treatment without separation. Similar behavior was observed for the potential production with a maximum of 0.41 m³ methane.kg-1 COD added with an HRT of 7 days without separation of the solid fraction. The separation of the solid fraction is not recommended in the pretreatment of liquid effluent from poultry slaughterhouse, once the potential for production and production of methane and biogas were reduced with this treatment

Avaliação de Três Cultivares de Panicum maximum Jacq. sob Pastejo: Composição Química e Digestibilidade da Forragem Evaluation of Three Cultivars of Panicum Maximum Jacq. under Grazing: Chemical Composition and in Vitro Organic Matter Digestibility

O estudo foi conduzido com o objetivo de estimar o valor nutritivo da MS de três cultivares de Panicum maximum Jacq. submetidas ao pastejo rotativo, através dos teores de proteína bruta, fibra em detergente neutro, fibra em detergente ácido, lignina, celulose, sílica e digestibilidade in vitro da matéria orgânica em amostras de folhas e colmos. Estudou-se, também, no cultivar Tanzânia, a adubação nitrogenada no final do período chuvoso, adicional à de manutenção comum às demais cultivares. As amostragens foram realizadas em junho, setembro e novembro de 1998 e março de 1999. Algumas diferenças entre tratamentos foram observadas, apresentando, em geral, menor valor nutritivo no cv. Massai, com menores teores de proteína bruta e digestibilidade e maiores teores de fibra em detergente neutro, fibra em detergente ácido e lignina tanto nas folhas, como nos colmos. Sua utilização como opção forrageira deve basear-se em outras características agronômicas. O cv. Mombaça apresentou, em geral, maiores teores de sílica e seu valor nutritivo não foi afetado pela adubação nitrogenada no final do período chuvoso, exceto pelo aumento no teor de proteína bruta e pela redução do conteúdo de lignina e sílica em março. O valor nutritivo dos colmos foi inferior ao das folhas. O início do período chuvoso foi, em geral, a época de maior valor nutritivo da forragem em todos os tratamentos.<br>A study was conducted to evaluate three cultivars of Panicum maximum Jacq. under rotational grazing for the nutritive value,where the estimates of crude protein, neutral detergent fiber, acid detergent fiber, lignin, cellulose, silica, and in vitro digestibility of the organic material were performed in samples of leaves and stems. Additional nitrogen was applied in cv. Tanzania at the end of the rainny season. Samples were taken in June, September, and October 1998 and in March 1999. Some differences among treatments were observed. In general, cv. Massai showed a lower nutritive value with lower crude protein and digestibility, and higher neutral detergent fiber, acid detergent fiber, and lignin, either in samples of leaves or in stems. Therefore, its utilization as a forage option should be based on other agronomic characteristics. The cv. Mombaça exhibited higher concentrations of silica and its nutritive value was not affected by nitrogen fertilization at the end of the rainny season, except for an increase in the percentage of crude protein and a reduction in the amount of lignin and silica in March. The nutritive value of the stems was inferior to the leaves. The nutritive value was highest in all treatments at the beginning of the rainny period