Rethinking Institutional Repository Strategies

At the spring 2017 CNI meeting in Albuquerque, New Mexico, we held an Executive Roundtable on the topic of Rethinking Institutional Repository Strategies. We knew this was a timely topic for many of our member institutions, and we anticipated that many CNI member institutions would seek to attend this roundtable. To meet the demand, we offered two sessions of the roundtable (with different institutions participating in each) on sequential days, and even then had to turn away many who expressed interest. At the main CNI meeting, CNI’s executive director Clifford Lynch offered a summary of the roundtables during one of the breakout sessions. This report expands upon the themes Lynch described and adds more details about participants’ observations and current activities

Pesquisa de demanda por informação tecnológica pelo setor produtivo

A Pesquisa de Demanda por Informação Tecnológica pelo Setor Produtivo, surgida no âmbito da Subcomissão de Informação Tecnológica do Programa de Apoio à Capacitação Tecnológica da Indústria (PACTI) e realizada em 1996, busca identificar as necessidades de informação por parte do setor industrial, com o objetivo de suprir as instituições/centros provedores de informação tecnológica com dados acerca do mercado demandante para que estes possam adequar melhor os seus produtos e serviços

Pesquisa de demanda por informação tecnológica pelo setor produtivo

A Pesquisa de Demanda por Informação Tecnológica pelo Setor Produtivo, surgida no âmbito da Subcomissão de Informação Tecnológica do Programa de Apoio à Capacitação Tecnológica da Indústria (PACTI) e realizada em 1996, busca identificar as necessidades de informação por parte do setor industrial, com o objetivo de suprir as instituições/centros provedores de informação tecnológica com dados acerca do mercado demandante para que estes possam adequar melhor os seus produtos e serviços

An evolutionarily young defense metabolite influences the root growth of plants via the ancient TOR signaling pathway.

To optimize fitness a plant should monitor its metabolism to appropriately control growth and defense. Primary metabolism can be measured by the universally conserved TOR (Target of Rapamycin) pathway to balance growth and development with the available energy and nutrients. Recent work suggests that plants may measure defense metabolites to potentially provide a strategy ensuring fast reallocation of resources to coordinate plant growth and defense. There is little understanding of mechanisms enabling defense metabolite signaling. To identify mechanisms of defense metabolite signaling, we used glucosinolates, an important class of plant defense metabolites. We report novel signaling properties specific to one distinct glucosinolate, 3-hydroxypropylglucosinolate across plants and fungi. This defense metabolite, or derived compounds, reversibly inhibits root growth and development. 3-hydroxypropylglucosinolate signaling functions via genes in the ancient TOR pathway. If this event is not unique, this raises the possibility that other evolutionarily new plant metabolites may link to ancient signaling pathways

The ARL/CNI 2035 Scenarios

L’ Association des bibliothèques de recherche (ARL) et la Coalition pour les réseaux Information (CNI) ont choisi d’appliquer la planification de scénarios pour imaginer un avenir influencé par l’intelligence artificielle (IA) et pour explorer l’étendue de l’incertitude liée à l’IA dans l’écosystème de la recherche et de la connaissance. Ces scénarios ont été développés dans une perspective nord-américaine grâce à un engagement profond avec le CNI membres de l’AR

RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3'UTR required for intermediate vancomycin resistance.

Treatment of methicillin-resistant Staphylococcus aureus infections is dependent on the efficacy of last-line antibiotics including vancomycin. Treatment failure is commonly linked to isolates with intermediate vancomycin resistance (termed VISA). These isolates have accumulated point mutations that collectively reduce vancomycin sensitivity, often by thickening the cell wall. Changes in regulatory small RNA expression have been correlated with antibiotic stress in VISA isolates however the functions of most RNA regulators is unknown. Here we capture RNA-RNA interactions associated with RNase III using CLASH. RNase III-CLASH uncovers hundreds of novel RNA-RNA interactions in vivo allowing functional characterisation of many sRNAs for the first time. Surprisingly, many mRNA-mRNA interactions are recovered and we find that an mRNA encoding a long 3' untranslated region (UTR) (termed vigR 3'UTR) functions as a regulatory 'hub' within the RNA-RNA interaction network. We demonstrate that the vigR 3'UTR promotes expression of folD and the cell wall lytic transglycosylase isaA through direct mRNA-mRNA base-pairing. Deletion of the vigR 3'UTR re-sensitised VISA to glycopeptide treatment and both isaA and vigR 3'UTR deletions impact cell wall thickness. Our results demonstrate the utility of RNase III-CLASH and indicate that S. aureus uses mRNA-mRNA interactions to co-ordinate gene expression more widely than previously appreciated

Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains

Metabolic engineering has been vital to the development of industrial microbes such as the yeast Saccharomyces cerevisiae. However, sequential rounds of modification are often needed to achieve particular industrial design targets. Systems biology approaches can aid in identifying genetic targets for modification through providing an integrated view of cellular physiology. Recently, research into the generation of commercial yeasts that can produce reduced-ethanol wines has resulted in metabolically-engineered strains of S. cerevisiae that are less efficient at producing ethanol from sugar. However, these modifications led to the concomitant production of off-flavour by-products. A combination of transcriptomics, proteomics and metabolomics was therefore used to investigate the physiological changes occurring in an engineered low-ethanol yeast strain during alcoholic fermentation. Integration of ‘omics data identified several metabolic reactions, including those related to the pyruvate node and redox homeostasis, as being significantly affected by the low-ethanol engineering methodology, and highlighted acetaldehyde and 2,4,5-trimethyl-1,3-dioxolane as the main off-flavour compounds. Gene remediation strategies were then successfully applied to decrease the formation of these by-products, while maintaining the ‘low-alcohol’ phenotype. The data generated from this comprehensive systems-based study will inform wine yeast strain development programmes, which, in turn, could potentially play an important role in assisting winemakers in their endeavour to produce low-alcohol wines with desirable flavour profiles

Persistent Chlamydia Pneumoniae serology is related to decline in lung function in women but not in men. Effect of persistent Chlamydia pneumoniae infection on lung function

<p>Abstract</p> <p>Background</p> <p><it>Chlamydia pneumoniae </it>(C pn) infection causes an acute inflammation in the respiratory system that may become persistent, but little is known about the long-term respiratory effects of C pn infections. Aim: To estimate the long term respiratory effects of C pn with change in forced expiratory volume in one second (FEV₁) and forced vital capacity (FVC) as a main outcome variable.</p> <p>Methods</p> <p>The study comprised of 1109 subjects (500 men and 609 women, mean age 28 ± 6 years) that participated in the Reykjavik Heart Study of the Young. Spirometry and blood samples for measurements of IgG antibodies for C pn were done at inclusion and at the end of the follow-up period (mean follow-up time 27 ± 4 years).</p> <p>Results</p> <p>Having IgG against C pn at both examinations was significantly associated to a larger decrease in FEV₁(6 mL/year) and FVC (7 mL/year) in women but not in men. In women the association between C pn and larger FEV₁decline was only found in women that smoked at baseline where having C pn IgG was associated with 10 mL/year decline compared to smokers without C pn IgG. These results were still significant after adjustment for age, smoking and change in body weight.</p> <p>Conclusion</p> <p>Our results indicate that persistent C pn serology is related to increased decline in lung function in women but not in men. This effect was, however, primarily found in smoking women. This study is a further indication that the pathophysiological process leading to lung impairment may differ between men and women.</p

PMeS: Prediction of Methylation Sites Based on Enhanced Feature Encoding Scheme

Protein methylation is predominantly found on lysine and arginine residues, and carries many important biological functions, including gene regulation and signal transduction. Given their important involvement in gene expression, protein methylation and their regulatory enzymes are implicated in a variety of human disease states such as cancer, coronary heart disease and neurodegenerative disorders. Thus, identification of methylation sites can be very helpful for the drug designs of various related diseases. In this study, we developed a method called PMeS to improve the prediction of protein methylation sites based on an enhanced feature encoding scheme and support vector machine. The enhanced feature encoding scheme was composed of the sparse property coding, normalized van der Waals volume, position weight amino acid composition and accessible surface area. The PMeS achieved a promising performance with a sensitivity of 92.45%, a specificity of 93.18%, an accuracy of 92.82% and a Matthew’s correlation coefficient of 85.69% for arginine as well as a sensitivity of 84.38%, a specificity of 93.94%, an accuracy of 89.16% and a Matthew’s correlation coefficient of 78.68% for lysine in 10-fold cross validation. Compared with other existing methods, the PMeS provides better predictive performance and greater robustness. It can be anticipated that the PMeS might be useful to guide future experiments needed to identify potential methylation sites in proteins of interest. The online service is available at http://bioinfo.ncu.edu.cn/inquiries_PMeS.aspx

Is Chinese Competition Causing Deindustrialization in Brazil?

There has been a lively debate in Brazil in recent years, involving sectors of business, the labor movement, and academics, over deindustrialization and the future of the manufacturing sector. This is often linked to the growing relation between Brazil and China, which is now the country’s most significant trade partner. Brazil has experienced relative deindustrialization in the sense of a declining share of the manufacturing sector in gross domestic product that is mainly attributable to the changes in the country’s trade balance in manufactures. The direct and indirect impacts of China on Brazilian manufacturing have contributed to this relative deindustrialization