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

Influence of hydrodynamics on the water pathway and spatial distribution of pesticide and metabolite concentrations in constructed wetlands

International audienceConstructed wetlands (CWs) are likely to reduce pesticide levels reaching surface water. However, the distri-bution of the water flow path between the main channel and isolated areas may influence global pesticide mitigation. Little information is known about the influence of water pathways on pesticide mitigation. Thus, we performed tracer experiments at low and high flow rates (0.5 L/s and 4–7 L/s) in a pond CW and ditch CW to determine the localization of various hydraulic zones and to understand their implication on pesticide mitiga-tion. The hydraulic performance reflecting the fraction of water transported from inlet to outlet passing through the whole of CW, was greater for the pond CW than for the ditch CW regardless of the flow rate, and greater at mean flow rates (MF) than at low flow rates (LF) due to a lower proportion of isolated areas at a MF (11%–68%) than at LF (38%–89%). Dispersion governed the water transport inside the isolated areas and the water con-vection inside the main channel. Consequently, dissolved pesticide concentrations are heterogeneously distrib-uted in the CWs, i.e., in the main channel and isolated area, for both flow rates. However, one month after a no- flow period, this heterogeneity disappears, and dissolved pesticide concentrations become similar in the water of the whole CW due to dispersion. Furthermore, sedimentation and storage in sediments were greater in the isolated area than in the main channel, which is possibly due to a lower speed flow rate and a higher hydraulic residence time (HRT) in the isolated area than in the main channel. Thus, isolated areas act as effective’s zones to mitigate pesticides from dissolved and particulate phases inside the CW during a complete drainage season (i.e., succession of high/low/no-flow periods

Wetland hydrodynamics and mitigation of pesticides and their metabolites at pilot-scale

International audienceConstructed wetlands (CWs) are useful for reducing pesticide transfer from drainage into surface water, though little was known about the influence of hydrodynamics on their mitigation. We thus assessed the influence of design parameters (aspect ratio, water depth, flow rate) on hydraulic performance simultaneously to pesticide mitigation. We performed our work on four pesticides with contrasted properties: boscalid (BSC), cyproconazole (CYP), isoproturon (IPU) and dimethachlor (DMT), under three controlled flow-rate conditions (including no-flow) by using two pilots with contrasted designs (pond and ditch) over 62 days. Hydraulic performance and pesticide mitigation were less effective in a pond than in the ditch whatever the flow. Moreover, pesticide mitigation was more significant at low than at high flow rates for both pilots. M high flow rate, water transport is mainly governed by convection, but at low flow rates both water transport and mitigation are governed by hydrodynamic dispersion, inducing a longer contact time between pesticides and substrate due to longer hydraulic retention. Finally, BSC and CYP are better mitigated than DMT and IPU, even if they are also more strongly released during low flow rates. In addition, the mitigation of pesticides and some of their metabolites produced inside the pilots was almost complete during stagnation

Structure of the Demerara passive-transform margin and associated sedimentary processes. Initial results from the IGUANES cruise

he IGUANES cruise took place in May 2013 on the R/V L'Atalante along the Demerara passive transform margin off French Guiana and Surinam. Seismic, multibeam and chirp acquisitions were made. Piston cores were collected for pore geochemistry and sedimentology. A mooring was deployed on the sea-bottom for 10 months (temperature, salinity, turbidity and current measurements). This new dataset highlights the lateral variability of the 350 km-long Guiana–Surinam transform margin due to the presence of a releasing bend between two transform segments. The adjacent Demerara Plateau is affected by a 350 km-long giant slide complex. This complex initiated in Cretaceous times and was regularly reactivated until recent times. Since the Miocene, contourite processes seem to be active due to the onset of the North Atlantic Deep Water (NADW) bottom current. A main NADW water vein flows towards SE, eroding slide headscarps and allowing the deposition of contourite drifts. Numerous depressions looking like comet tails or comet scours record this flow. Some of those were interpreted before the cruise as active pockmarks. Pore geochemistry and core analysis do not show any evidence of present-day gas seepage

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 science. © The Author(s) 2019. Published by Oxford University Press