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

Epidemiología de la enfermedad neumocócica invasiva en la región de Tarragona, 2012-2015: incidencia, letalidad y cobertura de serotipos para las distintas formulaciones vacunales antineumocócicas

ABSTRACT Background: Nowadays, after licensure of the second generation new pneumococcal conjugate vaccines (PCV10/PCV13). The epidemiology of the pneumococcal disease must be re-evaluated. The present study described incidence, lethality and serotype distribution of invasive pneumococcal disease (IPD) in the general population of Tarragona’s region (Spain) after licensure of these vaccines. Methods: Retrospective study that included all cases of IPD (pneumococcus isolated in sterile sites) diagnosed among all-age individuals in the Spanish region of Tarragona (Tarragonés, Alt Camp and Baix Penedés counties) from 01/01/2012 to 31/12/2015. Incidence and lethality rates were estimated by age strata and globally. Similarly, it was determined the prevalence of IPD cases caused by serotypes included in the distinct formulations of multivalent conjugate vaccines (pcv7), PCV10 and PCV13) or 23-valent polysaccharide vaccine (PPV23). Results: A total of 171 IPD cases were observed, which means a global incidence (per 100,000 persons-year) of 10.82 (7.86 in ≤14 years, 5.94 in 15-64 years and 36.46 in ≥65 years; p<0.001). Overall lethality rate was 6.8% (none in children, 9,3% in people 15-64 years and 6.9% in people ≥65 years). A serotype was identified in 132 (77.2%) of the 171 studied samples. Serotype-vaccine coverages (cases due to vaccine-type serotypes) were 14.4%, 26.5%, 42.4% and 78.8% for the PCV7, PCV10, PCV13 and PPV23, respectively (p<0.001). Conclusion: Incidence and lethality of IPD were intermediate-low in the region of Tarragona throughout 2012-2015. During this period, Serotype-vaccine coverage was almost double for the 23-valent than for the 13-valent vaccine.RESUMEN Fundamentos: En la actualidad, tras la comercialización de las nuevas vacunas neumocócicas conjugadas de segunda generación (VNC10/VNC13), la epidemiología de la enfermedad neumocócica debe ser reevaluada. El presente estudio tuvo como objetivo describir la incidencia, letalidad y distribución serotípica de la enfermedad neumocócica invasiva (ENI) en la población general del área de Tarragona durante el cuatrienio posterior a la introducción de estas vacunas. Métodos: Estudio observacional retrospectivo que incluyó todos los casos de ENI (Streptococcus pneumoniae aislado en sangre, líquido cefalorraquídeo, líquido pleural/articular/peritoneal o muestras de tejidos profundos obtenidas de forma estéril mediante punción-aspiración o biopsia) diagnosticados en el área de Tarragona (comarcas del Tarragonés, Alt Camp y Baix Penedés) entre 01/01/2012 y 31/12/2015. Se estimaron tasas de incidencia y letalidad (globalmente y por estratos etarios) y se determinó la prevalencia de casos causados por serotipos incluidos en las distintas formulaciones de vacunas antineumocócicas conjugadas heptavalente (VNC7), decavalente (VNC10), tridecavalente (VNC13) y polisacárida tricosavalente (VNP23). Resultados: Se observaron 171 casos de ENI, lo que representó una incidencia (por 100.000 personas-año) de 10,82 (7,86 en ≤14 años, 5,94 en 15-64 años y 36,46 en ≥65 años; p<0,001). La letalidad fue del 6,8% (ninguna en niños, 9,3% en 15-64 años y 6,9% en personas ≥65 años; p<0,001). El serotipo responsable fue identificado en 132 (77,2%) de las 171 muestras estudiadas. La cobertura serotípica (casos causados por serotipos vacunales) fue del 14,4%, 26,5%, 42,4% y 78,8% para la VNC7, VNC10, VNC13 y VNP23, respectivamente (p<0,001). Conclusiones: Durante el periodo 2012-2015 la incidencia y letalidad por ENI fue intermedia-baja en el área de Tarragona, destacando que la cobertura serotípica fue casi doble para la vacuna 23-valente que para la 13-valente

Drug-resistance in Streptococcus pneumoniae isolates among Spanish middle aged and older adults with community-acquired pneumonia

<p>Abstract</p> <p>Background</p> <p>Pneumococcal diseases remain a major cause of morbidity and mortality worldwide. Updated data on drug-resistance from different populations may be important to recognize changes in disease patterns. This study assessed current levels of penicilin resistance among <it>Streptococcus Pneumoniae </it>causing pneumonia in Spanish middle age and older adults.</p> <p>Methods</p> <p>Antimicrobial susceptibility was tested for 104 consecutive isolates of Streptococcus pneumoniae recovered from patients 50 years or older with radiographically confirmed pneumonia in the region of Tarragona (Spain) between 2002 and 2007. According to the minimum inhibitory concentration of tested antimicrobials (penicillin, erythromycin, cefotaxime and levofloxacin) strains were classified as susceptible or resistant. Antimicrobial resistance was determined for early cases (2002–2004) and contemporary cases (2005–2007).</p> <p>Results</p> <p>Twenty-seven (25.9%) were penicillin-resistant strains (19 strains with intermediate resistance and 8 strains with high resistance). Penicillin-resistance was higher in 2002–2004 than in 2005–2007 (39.5% vs 18.2%, p = 0.017).</p> <p>Of 27 penicillin-resistant strains, 10 (37%) were resistant to erythromycin, 8 (29.6%) to cefotaxime, 2 (7.4%) to levofloxacin, and 4 (14.8%) were identified as multidrug resistant. Case-fatality rate was higher among those patients who had an infection caused by any penicillin susceptible strain (16.9%) than in those with infections due to penicillin-resistant strains.</p> <p>Conclusion</p> <p>Resistance to penicillin among Streptococcus pneumoniae remains high, but such resistance does not result in increased mortality in patients with pneumococcal pneumonia.</p