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

Wind-driven monthly variations in transport and the flow field in the Faroe–Shetland Channel

The transport of water from the North Atlantic to the Nordic seas through the Faroe–Shetland Channel is analysed from a decade of conductivity, temperature and depth (CTD) and acoustic Doppler current profiler (ADCP) data. The long-term mean transport, integrated over the upper 500 m, is 3.5 } 0.1 Sv (1 Sv = 10 6 m 3 s ? 1 ), of which 2.1 Sv is barotropic flow and 1.4 Sv is baroclinic flow. Short-term variability leads to a standard deviation of ca. 2.2 Sv in 3-day averages of the ADCP-measured transport. The barotropic transport is located over the upper part of the slope region of the Shetland Shelf, but sometimes broadens over deeper water. There is a peak surface baroclinic transport above the foot of the slope, and a weak recirculation of Modified North Atlantic Water (MNAW), which enters from the north, on the Faroese side. In September, when isobars downwell on the eastern side, the strong transport (ca. 4 Sv) is barotropic and evenly distributed across the Shetland slope, and both recirculation of MNAW from the Faroe side and mesoscale activity are weak. In spring, the net transport is small (ca. 2.5 Sv), the MNAW recirculation is strong and mesoscale activity is relatively large. These seasonal variations appear to correlate with the local south-west wind stress, which may contribute to nearly half of the long-term transport in the channel

On the characteristics of internal tides and coastal upwelling behaviour in Marguerite Bay, west Antarctic Peninsula

Internal waves and coastal upwelling have important roles in both physical oceanography and marine ecosystems, via processes such as mixing of water masses and transfer of heat and nutrients to biologically-active layers. In this paper we use quasi-weekly hydrographic profiles and moored records of temperature, salinity and water velocity to investigate the nature of internal tides and coastal upwelling behaviour in northern Marguerite Bay at the western Antarctic Peninsula. Within Ryder Bay, a near-coastal site in northern Marguerite Bay, atmospherically-forced oscillations of the water column with periods around 2-7 days are observed, associated with wind-induced coastal upwelling and downwelling. Sea ice cover is seen to play a role in the seasonal suppression of these oscillations. Significant internal tides are also observed at this site. A range of processes are seen to be important in controlling internal tide variability, including changes in local stratification and sea ice conditions. Both diurnal and semi-diurnal internal tidal species are observed, despite the study region being poleward of the critical latitude for diurnal internal tides. This suggests that at least the diurnal internal tides are generated close to the study location, and we investigate likely sources. Our work adds understanding to how such phenomena are generated, and what controls their variability, in a region of rapid physical change and profound ecosystem importance

The impact of changes in North Atlantic Gyre distribution on water mass characteristics in the Rockall Trough

Regular time-series of temperature and salinity in the upper waters of the northern Rockall Trough can be traced back to 1948, when Ocean Weather Ships on passage to the west began to record them. Since 1975, these data have been complemented by, then replaced by, dedicated Conductivity, Temperature, and Depth sections along 57.5°N. Today, they are enhanced with real-time observations of the upper 1000 m made by an underwater glider. Since 1995, there has been a steady increase in both temperature (from 9.1 to 10°C) and salinity (from 35.32 to 35.41) as the Subpolar Gyre has retreated west. The historical record suggests that such increases could be compatible with decadal scales of natural variability. Nutrient (nitrate, phosphate, and silicate) concentrations have been measured systematically since 1996 and exhibit interannual variability, particularly in nitrate, the causes of which are not immediately clear. Average phosphate concentrations in the upper 800 m declined from 0.80 to 0.63 ?M by 2009, consistent with the recent incursion of depleted Subtropical Gyre water. The Ellett Line dataset contains a unique and essential archive of observations that can be used to place in context the recent changes in local ocean climate

Physical oceanography and hydrochemistry from the ICES NANSEN Project

This data collection contains water temperature, salinity, phosphate, nitrate, silicate, oxygen and chlorophyll values during 21 campaigns in the frame of the ICES NANSEN Project

Three arguments against ‘soft innovation’: towards a richer understanding of cultural innovation

This paper critiques recent research on innovation in the cultural and creative industries. In particular, this paper examines Paul Stoneman’s idea of ‘soft innovation’ as a jumping off point for discussing theories of cultural innovation more broadly. Three critiques are advanced. Firstly, soft innovation is a theoretical perspective that has developed from neoclassical economics, and is therefore vulnerable to criticisms levelled at neoclassical explanations of economic behaviour. Secondly, the theory of soft innovation can be criticised for being contin- gently inaccurate: the observed reality of cultural industries and marketplaces may not reflect the theory’s premises. Thirdly, because soft innovation defines the significance of an innovation in terms of marketplace success, it implies that only high-selling cultural products are significant, a difficult claim to substantiate. This paper concludes by arguing that our understanding of innovation in the cultural sphere can benefit from a multi-disciplinary approach grounded in the full gamut of human creativity