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

Modelling of a New Thermal Compressor for Supercritical CO2 Heat Pump

ACLInternational audienc

Influence des volumes morts sur les performances d’un nouveau concept de compresseur thermique

ACTNational audienc

A new heat driven compressor for heat pump application

ACTInternational audienc

Modelling of a New Thermal Compressor for Supercritical CO2 Heat Pump

International audienceA new concept of thermal compressor has been designed by the boostHEAT company. This compressor uses thermal energy provided through the heater instead of mechanical energy to increase the pressure of the heat pump working fluid. The compressor is made up by the following pts: A cylinder with a displacer piston, a heater, a regenerator and a cooler. The heater is connected to the hot pt of the cylinder on the one hand and to the regenerator on the other hand. The cooler is connected to the regenerator on the one hand and to the cold pt of the cylinder on the other hand. The cold pt of the cylinder is connected to the low pressure branch of the heat pump (evaporator) through an automatic inlet valve, and to the high pressure branch of the heat pump (gas cooler) through an automatic exhaust valve. The compressor is intended to replace the conventional mechanical compressor in a CO2 heat pump for the residential heating or combined heat and power mket. The main feature of the system is that the working fluid of the thermal engine for compression is the same as the working fluid of the heat pump. The principle of the new thermal compressor and its advantages for heat pump application will be briefly presented. A model of the thermal compressor has been developed. Modelling results related to the regenerator, the piston rod diameter, the size of the adiabatic dead volumes and the working fluid leaks in the annul gap between the cylinder liner and the piston e presented

VpStyA1/VpStyA2B of Variovorax paradoxus EPS: An Aryl Alkyl Sulfoxidase Rather than a Styrene Epoxidizing Monooxygenase

Herein we describe the first representative of an E2-type two-component styrene monooxygenase of proteobacteria. It comprises a single epoxidase protein (VpStyA1) and a two domain protein (VpStyA2B) harboring an epoxidase (A2) and a FAD-reductase (B) domain. It was annotated as VpStyA1/VpStyA2B of Variovorax paradoxus EPS. VpStyA2B serves mainly as NADH:FAD-oxidoreductase. A Km of 33.6 ± 4.0 µM for FAD and a kcat of 22.3 ± 1.1 s−1 were determined and resulted in a catalytic efficiency (kcat Km−1) of 0.64 s−1 μM−1. To investigate its NADH:FAD-oxidoreductase function the linker between A2- and B-domain (AREAV) was mutated. One mutant (AAAAA) showed 18.7-fold higher affinity for FAD (kcat Km−1 of 5.21 s−1 μM−1) while keeping wildtype NADH-affinity and -oxidation activity. Both components, VpStyA2B and VpStyA1, showed monooxygenase activity on styrene of 0.14 U mg−1 and 0.46 U mg−1, as well as on benzyl methyl sulfide of 1.62 U mg−1 and 3.11 U mg−1, respectively. The high sulfoxidase activity was the reason to test several thioanisole-like substrates in biotransformations. VpStyA1 showed high substrate conversions (up to 95% in 2 h) and produced dominantly (S)-enantiomeric sulfoxides of all tested substrates. The AAAAA-mutant showed a 1.6-fold increased monooxygenase activity. In comparison, the GQWCSQY-mutant did neither show monooxygenase nor efficient FAD-reductase activity. Hence, the linker between the two domains of VpStyA2B has effects on the reductase as well as on the monooxygenase performance. Overall, this monooxygenase represents a promising candidate for biocatalyst development and studying natural fusion proteins