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

Transcriptional Profiling of Serogroup B Neisseria meningitidis Growing in Human Blood: An Approach to Vaccine Antigen Discovery

Neisseria meningitidis is a nasopharyngeal commensal of humans which occasionally invades the blood to cause septicaemia. The transcriptome of N. meningitidis strain MC58 grown in human blood for up to 4 hours was determined and around 10% of the genome was found to be differentially regulated. The nuo, pet and atp operons, involved in energy metabolism, were up-regulated, while many house-keeping genes were down-regulated. Genes encoding protein chaperones and proteases, involved in the stress response; complement resistant genes encoding enzymes for LOS sialylation and biosynthesis; and fHbp (NMB1870) and nspA (NMB0663), encoding vaccine candidates, were all up-regulated. Genes for glutamate uptake and metabolism, and biosynthesis of purine and pyrimidine were also up-regulated. Blood grown meningococci are under stress and undergo a metabolic adaptation and energy conservation strategy. The localisation of four putative outer membrane proteins encoded by genes found to be up-regulated in blood was assessed by FACS using polyclonal mouse antisera, and one (NMB0390) showed evidence of surface expression, supporting its vaccine candidacy

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

Impact of 3D cell culture on bone regeneration potential of mesenchymal stromal cells

As populations age across the world, osteoporosis and osteoporosis-related fractures are becoming the most prevalent degenerative bone diseases. More than 75 million patients suffer from osteoporosis in the US, the EU and Japan. Furthermore, it is anticipated that the number of patients affected by osteoporosis will increase by a third by 2050. Although conventional therapies including bisphosphonates, calcitonin and oestrogen-like drugs can be used to treat degenerative diseases, they are often associated with serious side effects including the development of oesophageal cancer, ocular inflammation, severe musculoskeletal pain, and osteonecrosis of the jaw. The use of autologous mesenchymal stromal cells/mesenchymal stem cells (MSCs) is a possible alternative therapeutic approach to tackle osteoporosis while overcoming the limitations of traditional treatment options. However, osteoporosis can cause a decrease in the numbers of MSCs, induce their senescence, and lower their osteogenic differentiation potential. Three-dimensional (3D) cell culture is an emerging technology that allows a more physiological expansion and differentiation of stem cells compared to cultivation on conventional flat systems. This review will discuss current understanding of the effects of different 3D cell culture systems on proliferation, viability, osteogenic differentiation, as well as on the immunomodulatory and anti-inflammatory potential of MSCs

Drilling engineering experience gained from MD-BTES construction phase of SKEWS demo-site

As a result of the current energy crisis triggered by war and increasing shortage of resources, renewable energy sources are becoming increasingly important. The storage of heat from fluctuating energy sources is an essential component for independent and base-load capable energy supply. A promising technology are medium-deep geothermal storage systems, which store excess heat in the crystalline subsurface and offer significant advantages over near-surface geothermal storage systems. At the Lichtwiese campus of the Technical University of Darmstadt, the world's first medium-deep research geothermal storage system was constructed in the crystalline bedrock with three 750 m deep boreholes with a distance of approx. 8.6 m (research project SKEWS, project administrator Jülich, funding code 03EE4030A). The outer casing of the coaxial system has a diameter of 7", on which an attached glass fiber cable records temperature and strain measurements. Research operations began in the spring of 2023, which consists of an initial enhanced Geothermal Response Test (eGRT) followed by five heating and cooling phases. The experience and knowledge acquired are intended to demonstrate the basic construction and operational feasibility of such storage systems, as well as to be used as a basis for the planning, dimensioning, construction and costing of future projects. With the current project status, it has already been possible to evaluate the processes of the drilling phase and their effects on the drilling operation. The encountering of deviating geological and hydrogeological conditions to the prognosis from the planning phase required, among other things, the change of the drilling technique from water hammer to rotary drilling with a clay-fresh-water fluid and accordingly also affected the verticality of the drillings. Based on the detailed drilling data recorded and the geological conditions explored, the drilling phase of the storage system could be evaluated in terms of its material usage, drilling accuracy, costs and energy consumption

Why journalists covered Syria the way they did: On the role of economic, social and cultural capital

While recent decades have seen the rise of a vast body of work on war reporting, there have been few sociological explanations of why journalists deal with challenging situations in particular ways. This article contributes to bridging the gap between practice-based studies of war reporting and general sociological studies of journalism as a profession, by providing a systematically sociological account of the factors that influenced how the Syrian conflict was covered by Dutch and Flemish reporters working for a wide range of media. In doing so, this article draws on 13 in-depth interviews with those reporters, which is informed by a content analysis of their work, and Pierre Bourdieu’s concepts of economic, social and cultural capital on both an institutional and an individual level. In addition, it is argued that Bourdieusian analyses may be developed further by distinguishing between endogenous and exogenous forms of cultural capital