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

The comparison of the effect of conversation and conventional management systems on some parameters of soil biological activity under different soil-climatic conditions in Poland

Wyniki uzyskane podczas badań wykazały bardziej korzystne oddziaływanie konserwujących technologii uprawy, szczególnie technologii siewu bezpośredniego na środowisko glebowe, w porównaniu z technologią tradycyjną. Gleba uprawiana w technologii siewu bezpośredniego TSB w GR Rogów wykazywała wyższą zawartość C w biomasie mikroorganizmów o średnio około 13% oraz wyższą aktywność dehydrogenaz o średnio około 1,3 raza w porównaniu z technologią tradycyjną TT. Podobne różnice w wartościach badanych parametrów aktywności mikrobiologicznej gleby pomiędzy technologią konserwującą i tradycyjną obserwowano także w RZD Żelisławki. Stosunek C biomasy do C org. w glebie zarówno w Rogowie, jak i w Żelisławkach był wyższy w glebie uprawianej w siewie bezpośrednim TSB niż w systemie tradycyjnym TT.The main objective of the studies was to determine the effect of reduced tillage and direct sowing management systems on the changes of analyzed parameters of soil biological activity, in comparison to the changes in soil under conventional management system. At private farm Rogow, soil under direct sowing showed on average about 13,0 % higher contents of microbial biomass C, and 1,3 times higher activity of dehydrogenases system, than soil managed conventionally. Similar effects of direct sowing management on analyzed parameters of soil biological activity was observed at the Experimental Station Zelislawki. The calculated values of microbial quotient (C biomass : org. C ratio) for soils under direct sowing management were higher than values obtained for soil managed conventionally at both experimental sites, in 2003 and 2005. Significant increase in microbial quotient was noticed in 2005 as compared to 2003 at both experimental sites

Soil biological activity as affected by tillage intensity

The effect of tillage intensity on changes of microbiological activity and content of particulate organic matter in soil under winter wheat duirng 3 years was studied. Microbial response related to the tillage-induced changes in soil determined on the content of biomass C and N, the rate of CO2 evolution, B/F ratio, the activity of dehydrogenases, acid and alkaline phosphatases, soil C/N ratio and microbial biomass C/N ratio confirmed the high sensitivity of soil microbial populations to the tillage system applied. After three year studies, the direct sowing system enhanced the increase of labile fraction of organic matter content in soil. There were no significant changes in the labile fraction quantity observed in soil under conventional tillage. Similar response related to the tillage intensity was observed in particulate organic matter quantities expressed as a percentage of total organic matter in soil. A high correlation coefficients calculated between contents of soil microbial biomass C and N, particulate organic matter and potentiallymineralizable N, and the obtained yields of winter wheat grown on experimental fields indicated on a high importance of biological quality of status of soil for agricultural crop production

Activity of dehydrogenases as an indicator of soil environment quality

Activity of dehydrogenases (DHs) indicates the presence of viable and physiologically active (physiologically active or physiological activity) microorganisms. Their presence (activity) in soil is correlated with the content of organic carbon, microorganisms, nitrifying activity and microbial respiration. Determination of DHs activity allows to control changes in soil microbial population and is considered as an important parameter of soil quality. The aim of the study was to determine the effects of different farming systems on the enzymatic activity in soil under winter wheat. The research was conducted in the years 2014–2016 on long-term field experiment under two different farming systems (ecological and conventional) at the IUNG (PIB) Experimental Station located in Osiny (Lublin Voivodeship), Poland. Each farming system differs in crop rotation system and whole agrotechnics, which have been adapted to its specificity. Determination of DHs activity was performed using Casida et al.’s (1964) method with modifications. Measured DHs activity was expressed in milligrams of triphenyl formazan (TPF) per 100 g of soil within 24 hours. The results showed that ecological farming system beneficially influenced soil environment

Changes in soil quality associated with tillage system applied

The aim of this research was to evaluate changes in soil quality associated with the tillage system applied with chosen parameters of soil biological properties. The long-term field experiments were located at a private farm in Rogów (Zamooeæ region, E Poland) on a silt soil and at the Experimental Station in Laskowice (Wroc³aw region, S-W Poland) on a sandy loam soil. Soil samples were collected from 0-15 and 15-30 cm layers. Winter wheat was grown under traditional, reduced and no-tillage systems. The analyses included estimations of microbial biomass C and N content, microbial respiration rate, activity of dehydrogenase and arylsulfatase, and fluorescein diacetate hydrolysis. After eight years the effects of tillage on both soils were clearly noticed. In general, the less disturbing tillage systems enhanced the increase of soil biological activity by 15-40%, on average, than conventional tillage system. The significant correlations between microbial biomass, and/or enzyme activities with total organic C content indicate that concentration of organic C in soil environment plays an extremely important role in enhancing the stabilization and activity of soil microorganisms, and protection of an extracellular enzymes. The studied parameters of soil biological activity showed their sensitivity to tillage applied and may be considered as an useful indicators of soil quality in monitoring all conditions alter soil environment