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

Dissecting the theory-practice gap - A study of the capital budgeting processes of large Swedish Industrial Machinery firms

A firm’s success depends on its ability to allocate capital to productive use. This is carried out through a process referred to as capital budgeting. Previous research shows that the theory-preferred sophisticated Capital Budgeting Techniques (CBT) are becoming increasingly popular with time but that European and Swedish Industrial Engineering firms in particular to a great extent still use less sophisticated CBT. Reasons behind this gap have not been identified by the academic world, which constitutes an academic problem. Purpose The purpose of this study is to investigate the underlying reasons to a potential theory-practice gap within the firms included in the study. The study is intended as a complement to previous research of an explanatory nature and as input to further research in the area where identified reasons can be useful. Method The study is of a qualitative nature as this approach is better suited for capturing the various complex reasons affecting the design of a capital budgeting process. The methodology components consist of a literature study, containing both corporate finance theory and previous research and an empirical study of four interviews. The firms are evaluated on four components, cost of capital, CBT, risk and project characteristics. Further, only tangible projects in the production process are considered due to research quality reasons. The interviewed firms are all part of the Industrial Engineering industry’s sub-industry, the Industrial Machinery industry and listed on the Nasdaq OMX 30 index. Results and study findings The study has identified a theory-practice gap within the firms investigated. All firms employ a more or less fixed cost of capital for the firm, not reflecting the true cost of capital. In line with previous research, we find a great reliance on the payback-technique as an actual decision measure even though it is often combined with more sophisticated CBT. Risk is almost exclusively assessed qualitatively and only one firm incorporates risk in the CBT. Strategic value of a project affects the process as numerical criteria are lowered but is not valued using theoretical approaches. Flexibility is handled in a similar manner. We identify the main reason to the gap to be the priority of the capital budgeting process. Only limited evaluation and enhancements of the process are made which impedes firms to find all projects adding to firm value. The fundamental strategy of corporate finance theory that all projects with Net Present Value greater than zero should be undertaken seems to be overlooked. Future areas of research An obvious extension of this research would be to look at the investment process for all project types. Other possible future areas for research are similar studies in other industries in order to identify further reasons to a theory-practice gap. It is also of interest to perform research with a quantitative approach to investigate whether the findings can be generalized within the industry or country. Interesting research would also be to investigate the hypothetical relationship between reward systems based short-term profitability and capital budgeting practices

Development and evaluation of spherical molecularly imprinted polymer beads.

The majority of studies on molecularly imprinted polymers has until now been carried out on irregularly shaped particles prepared by grinding of polymer monoliths. The preparation procedures are time- and labor-consuming and produce particles of wide size distributions. To answer the need for fast and straightforward routes to spherical molecularly imprinted polymer beads, we have developed a method comprising the formation of droplets of pre-polymerization solution directly in mineral oil by vigorous mixing followed by transformation of the droplets into solid spherical beads by photoinduced free-radical polymerization. No detergents or stabilizers were required for the droplet formation. Factors influencing the bead synthesis have been investigated and are detailed here. The beads were evaluated in parallel with corresponding irregularly shaped particles prepared from polymer monoliths. Conditions for the synthesis of propranolol-imprinted poly(methacrylic acid-co-trimethylolpropane trimethacrylate) beads in the size range of 1-100 m in almost quantitative yield are described. The beads were applied as the recognition element in a 96-well plate format radioligand assay of propranolol in human serum

Influence of salt ions on binding to molecularly imprinted polymers.

Salt ions were found to have an influence on template binding to two model molecularly imprinted polymers (MIPs), targeted to penicillin G and propranolol, respectively, in water-acetonitrile mixtures. Water was detrimental to rebinding of penicillin G whereas propranolol bound in the entire water-acetonitrile range tested. In 100% aqueous solution, 3-M salt solutions augmented the binding of both templates. The effects followed the Hofmeister series with kosmotropic ions promoting the largest increase. Binding was mainly of a non-specific nature under these conditions. In acetonitrile containing low amounts of water, the specific binding to the MIPs increased with the addition of salts. Binding of penicillin G followed the Hofmeister series while an ion-exchange mechanism was observed for propranolol. The results suggest that hydration of kosmotropic ions reduces the water activity in water-poor media providing a stabilizing effect on water-sensitive MIP-template interactions. The effects were utilized to develop a procedure for molecularly imprinted solid-phase extraction (MISPE) of penicillin G from milk with a recovery of 87%