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

Spontaneous poisoning by Ricinus communis (Euphorbiaceae) in cattle

The aim of this study is to report cases of spontaneous poisoning of cattle by Ricinus communis (castor beans) in Paraíba, a semiarid region of northeastern Brazil. The cases were observed in 2 herds on neighboring properties in 2013. Clinical signs developed within 6-24 h and consisted of weakness, tachycardia, dyspnea, profuse watery diarrhea, dehydration, depression, instability, cramps, permanent lateral recumbency and death within 48-72 h. Of the 60 cattle at risk, 19 were affected and 14 died. Five fully recovered after the course of 12 days. Three animals were necropsied. The main gross lesions were hemopericardium, hemothorax, pulmonary edema, petechial hemorrhages in the epicardium and endocardium, ecchymoses at the papillary muscles and suffusions on the intercostal muscles. Hemorrhages were also observed in the abdominal cavity, spleen and mucosa of the abomasum and small intestine. The rumen content was liquid with a large amount of castor bean seeds. There were circular, whitish and focally diffuse areas in the liver parenchyma. The main microscopic lesions consisted of multifocal coagulative myocardial necrosis with the presence of mononuclear cell infiltration and varying degrees of bleeding between cardiac muscle fibers. The abomasum and small intestine mucosae and submucosa had mild edema and mononuclear and polymorphonuclear inflammatory cell infiltration. The diagnosis of R. communis was based on the history of plant consumption, clinical signs, pathology of the disease and the presence of large amounts of castor bean seeds in the forestomachs

Fibrose cardíaca associada à intoxicação por Amorimia septentrionalis em bovinos

Amorimia septentrionalis contém monofluoracetato de sódio e quando consumida por ruminantes provoca morte súbita. Este estudo teve o objetivo de relatar a epidemiologia, os sinais clínicos e patológicos de surtos de morte súbita em bovinos provocadas por Amorimia septentrionalis nos Estados de Pernambuco e Paraíba. Para isso, realizaram-se visitas técnicas em diversas propriedades nas Microrregiões do Médio Capibaribe/PE e Itabaiana/PB. Oito bovinos foram necropsiados. Coletaram-se tecidos das cavidades abdominal e torácica, além do encéfalo e medula espinhal. As alterações clínicas consistiram em lentidão, decúbito esternal prolongado, relutância em se movimentar quando em estação, cansaço, taquipneia, taquicardia e pulso venoso positivo. Os bovinos que foram forçados a se movimentar apresentaram instabilidade, tremores musculares e queda repentina seguida de vocalizações, movimentos de pedalagem e morte súbita em cerca de 5 a 7 minutos. As principais alterações macroscópicas consistiram em edema pulmonar, coração com aspecto globular com áreas esbranquiçadas, petéquias e equimoses no epicárdio, miocárdio e músculos papilares. À microscopia observou-se aumento da eosinofilia do citoplasma dos cardiomiócitos, núcleos picnóticos, cariorrexia, cariólise, perda das estriações, edema intersticial, infiltrado inflamatório intersticial mononuclear e áreas multifocais de fibrose cardíaca. Nos rins, constatou-se degeneração hidrópico vacuolar e necrose das células epiteliais em túbulos contorcidos. Os sinais clínicos foram semelhantes aos sinais clínicos já descritos em bovinos por plantas que contém MFA. As lesões macro e microscópicas descritas no coração e rins são de grande valor diagnóstico. A. septentrionalis é a principal planta tóxica de interesse pecuário nas microrregiões do Médio Capibaribe e Itabaiana devido às perdas econômicas diretas e indiretas que provoca na pecuária dessas regiões

Genetic variability of Pantaneiro horse using RAPD-PCR markers Variabilidade genética do cavalo Pantaneiro utilizando marcadores RAPD-PCR

Blood samples were collected from Pantaneiro Horses in five regions of Mato Grosso do Sul and Mato Grosso States. Arabian, Mangalarga Marchador and Thoroughbred were also included to estimate genetic distances and the existing variability among and within these breeds by RAPD-PCR (Random Amplified Polymorphic DNA - Polymerase Chain Reaction) molecular markers. From 146 primers, 13 were chosen for amplification and 44 polymorphic bands were generated. The analysis of molecular variance (AMOVA) indicated that the greatest portion of detected variability was due to differences between individuals within populations (75.47%). Analysis of the genetic variability between pairs of populations presented higher estimates for the five Pantaneiro populations with the Arabian breed, while lowest estimates were presented by pairs formed among the Pantaneiro populations with the Mangalarga Marchador. Highest genic diversity was shown by the Pantaneiro (0.3396), which also showed highest genetic distance with the Arabian and lowest with Mangalarga Marchador breed. UPGMA dendrogram showed distinct differences between naturalized (Pantaneiro and Mangalarga Marchador) and exotic (Arabian and Thoroughbred) breeds. In the dendrogram generated by UPGMA method, the similarity matrix generated by the Jaccard coefficient showed distinction between the naturalised breeds, Pantaneiro and Mangalarga Marchador, and the exotic breeds, Árab and English Thoroughbred. Results suggest that the Pantaneiro presents a higher genetic variability than the other studied breeds and has a close relationship with the Mangalarga Marchador.<br>Amostras de sangue foram coletadas de cavalos Pantaneiros de cinco regiões dos estados de Mato Grosso do Sul e Mato Grosso. As raças Mangalarga Marchador, Árabe e Puro-Sangue Inglês (PSI) usando marcadores moleculares RAPD-PCR (Random Amplified Polymorphic DNA - Polymerase Chain Reaction) foram incluídas no intuito de se calcular as distâncias genéticas e comparar a variabilidade genética entre e dentro de cada uma das raças. Dos 146 primers escrutinados, 13 foram escolhidos para amplificação com cada um dos indivíduos das oito populações, gerando um total de 44 bandas polimórficas. Os resultados encontrados na Análise de Variância Molecular (AMOVA) indicam que grande parte da variabilidade genética detectada se deve a diferenças entre indivíduos dentro de populações (75,47%). Na análise da estimativa dos percentuais de variabilidade genética entre pares de populações, foram observados maiores valores para os pares formados entre as cinco populações de cavalo Pantaneiro e a raça Árabe, enquanto os menores percentuais ocorreram entre Pantaneiro e Mangalarga Marchador. Maior índice de diversidade gênica foi observado na raça Pantaneiro (0,3396). No dendrograma gerado pelo método UPGMA, a partir da matriz de similaridade obtida pelo coeficiente de Jaccard, houve distinção entre as raças naturalizadas (Pantaneiro e Mangalarga Marchador) e as exóticas (Árabe e PSI). Os resultados encontrados sugerem que o Pantaneiro apresenta maior variabilidade genética que os de outras raças e está estreitamente relacionado ao Mangalarga Marchador