ERAWATCH Country Reports 2011: SWEDEN

The main objective of the ERAWATCH Annual Country Reports is to characterise and assess the performance of national research systems and related policies in a structured manner that is comparable across countries. EW Country Reports 2011 identify the structural challenges faced by national innovation systems. They further analyse and assess the ability of the policy mix in place to consistently and efficiently tackle these challenges. The annex of the reports gives an overview of the latest national policy efforts towards the enhancement of European Research Area and further assess their efficiency to achieve the targets. These reports were originally produced in November - December 2011, focusing on policy developments over the previous twelve months. The reports were produced by the ERAWATCH Network under contract to JRC-IPTS. The analytical framework and the structure of the reports have been developed by the Institute for Prospective Technological Studies of the Joint Research Centre (JRC-IPTS) and Directorate General for Research and Innovation with contributions from ERAWATCH Network Asbl.JRC.J.2-Knowledge for Growt

Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery

Viral infections cause many different diseases stemming both from well-characterized viral pathogens but also from emerging viruses, and the search for novel viruses continues to be of great importance. High-throughput sequencing is an important technology for this purpose. However, viral nucleic acids often constitute a minute proportion of the total genetic material in a sample from infected tissue. Techniques to enrich viral targets in high-throughput sequencing have been reported, but the sensitivity of such methods is not well established. This study compares different library preparation techniques targeting both DNA and RNA with and without virion enrichment. By optimizing the selection of intact virus particles, both by physical and enzymatic approaches, we assessed the effectiveness of the specific enrichment of viral sequences as compared to non-enriched sample preparations by selectively looking for and counting read sequences obtained from shotgun sequencing. Using shotgun sequencing of total DNA or RNA, viral targets were detected at concentrations corresponding to the predicted level, providing a foundation for estimating the effectiveness of virion enrichment. Virion enrichment typically produced a 1000-fold increase in the proportion of DNA virus sequences. For RNA virions the gain was less pronounced with a maximum 13-fold increase. This enrichment varied between the different sample concentrations, with no clear trend. Despite that less sequencing was required to identify target sequences, it was not evident from our data that a lower detection level was achieved by virion enrichment compared to shotgun sequencing

<i>Propionibacterium acnes: </i>disease-causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing

Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions but is also a proven contaminant of human clinical samples and surgical wounds. Its significance as a pathogen is consequently a matter of debate. In the present study, we investigated the presence of P. acnes DNA in 250 next-generation sequencing data sets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were subjected to either microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun sequencing. We detected high proportions of P. acnes DNA in enriched samples, particularly skin tissue-derived and other tissue samples, with the levels being higher in enriched samples than in shotgun-sequenced samples. P. acnes reads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show that P. acnes can be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. The possibility of contamination from the patient or other sources, including laboratory reagents or environment, should therefore always be considered carefully when P. acnes is detected in clinical samples. We advocate that detection of P. acnes always be accompanied by experiments validating the association between this bacterium and any clinical condition

Cutavirus in cutaneous malignant melanoma

A novel human protoparvovirus related to human bufavirus and preliminarily named cutavirus has been discovered. We detected cutavirus in a sample of cutaneous malignant melanoma by using viral enrichment and high-throughput sequencing. The role of cutaviruses in cutaneous cancers remains to be investigated

“The people who are out of ‘right’ English”: Japanese university students' social evaluations of English language diversity and the internationalisation of Japanese higher education

Previous research indicates that evaluations of speech forms reflect stereotypes of, and attitudes towards, the perceived group(s) of speakers of the language/variety under consideration. This study, employing both implicit and explicit attitude measures, investigates 158 Japanese university students' perceptions of forms of UK, US, Japanese, Chinese, Thai and Indian English speech. The results show a general convergence between students' explicit and implicit attitudes, for instance, regarding US and UK English as the most correct, and solidarity with Japanese speakers of English. The findings are discussed in relation to intergroup relations between the traditional Japanese cohort and specific groups of overseas students, particularly in light of recent internationalisation policies adopted by many Japanese universities, and the resultant increase in international students from South and East Asia

Identification of known and novel recurrent viral sequences in data from multiple patients and multiple cancers

Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified

Seizing the window of opportunity? The Swedish public innovation system’s support to private business in the early Covid-19 pandemic

This paper investigates the Swedish public innovation system’s response to the Covid-19 pandemic during 2020 in terms of initiatives targeting private business. It is based on a review of the websites of 181 major national and regional organisations in the Swedish public innovation system. A total of 208 initiatives were observed. The study shows that almost all national agencies and regional councils responded, but among more specialised organisations the response was scattered. The responses were on general rather swift, and most of them concerned short term crisis management. Initiatives to build long-term strength, e.g. re-skilling or platforms for potentially more radical renewal, were much fewer and often thematically unspecified. There is a moderately strong correlation between region size and response, but also regional differences on other dimensions, for example, regions strong in innovation involved expertise in specialised innovation support organisations to a much higher extent than other. Almost all university response came from ‘young’ universities. The largest and most research-intensive universities are almost absent in the material. Policy implications focus on the need to strengthen the innovation system’s capacity to be agile and initiate support initiatives with long-term perspectives in times of crisis. 

Working Together : Exploring Relational Tensions in Swedish Academia

This study explores the basic social conditions for high-quality university research, and focuses on research in science and technology in Sweden. Swedish research policy has adopted more of a market perspective on academic research and its role in society. This has meant the promotion of competition between researchers, increased focus on efficiency at universities, and attempts to make academia harmonize more with industry and other actors. How do such policies affect the variety of perspectives within the academic system? How do they affect the positions and identities of individual academics? These issues are discussed through the concept of "relational tensions". Relational tensions refer to social strains arising when interacting actors have different perspectives. Relational tensions can stimulate creativity, but may also cause unproductive conflicts. The discussion is underpinned by interviews with university researchers and a case study of Uppsala BIO-X, a program to commercialize university research in biotechnology. Typical cases of relational tensions are identified. These concern both interpersonal relations and differences between organized science and industry. A notable observation concerns potential frustration of individual academics, as competition and efficiency tends to make their positions and identities more contested. Researchers cope with relational tensions in three identified ways: socialization, seclusion, and lateral authority. Socialization is natural and often necessary, but reduces the variety of perspectives. Seclusion serves to retain variety and independence, but reduces interaction with others. Lateral authority is to formally or informally lend a researcher more authority, which improves the chance of maintaining a variety of perspectives without reducing interaction. The sustained usefulness of academic research arguably depends on its ability to foster and communicate a variety of perspectives. Hence, (i) promoting lateral authority seems fruitful within academia and in relations between academia and industry, and (ii) encouraging competition and efficiency may to some extent be counterproductive.Research Excellence and Science-Based Industrial System

Seizing the window of opportunity? The Swedish public innovation system’s support to private business in the early Covid-19 pandemic

This paper investigates the Swedish public innovation system’s response to the Covid-19 pandemic during 2020 in terms of initiatives targeting private business. It is based on a review of the websites of 181 major national and regional organisations in the Swedish public innovation system. A total of 208 initiatives were observed. The study shows that almost all national agencies and regional councils responded, but among more specialised organisations the response was scattered. The responses were on general rather swift, and most of them concerned short term crisis management. Initiatives to build long-term strength, e.g. re-skilling or platforms for potentially more radical renewal, were much fewer and often thematically unspecified. There is a moderately strong correlation between region size and response, but also regional differences on other dimensions, for example, regions strong in innovation involved expertise in specialised innovation support organisations to a much higher extent than other. Almost all university response came from ‘young’ universities. The largest and most research-intensive universities are almost absent in the material. Policy implications focus on the need to strengthen the innovation system’s capacity to be agile and initiate support initiatives with long-term perspectives in times of crisis.