Optimizing identification of clinically relevant gram-positive organisms by use of the bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) can be used as a method for the rapid identification of microorganisms. This study evaluated the Bruker Biotyper (MALDI-TOF MS) system for the identification of clinically relevant Gram-positive organisms. We tested 239 aerobic Gram-positive organisms isolated from clinical specimens. We evaluated 4 direct-smear methods, including “heavy” (H) and “light” (L) smears, with and without a 1-μl direct formic acid (FA) overlay. The quality measure assigned to a MALDI-TOF MS identification is a numerical value or “score.” We found that a heavy smear with a formic acid overlay (H+FA) produced optimal MALDI-TOF MS identification scores and the highest percentage of correctly identified organisms. Using a score of ≥2.0, we identified 183 of the 239 isolates (76.6%) to the genus level, and of the 181 isolates resolved to the species level, 141 isolates (77.9%) were correctly identified. To maximize the number of correct identifications while minimizing misidentifications, the data were analyzed using a score of ≥1.7 for genus- and species-level identification. Using this score, 220 of the 239 isolates (92.1%) were identified to the genus level, and of the 181 isolates resolved to the species level, 167 isolates (92.2%) could be assigned an accurate species identification. We also evaluated a subset of isolates for preanalytic factors that might influence MALDI-TOF MS identification. Frequent subcultures increased the number of unidentified isolates. Incubation temperatures and subcultures of the media did not alter the rate of identification. These data define the ideal bacterial preparation, identification score, and medium conditions for optimal identification of Gram-positive bacteria by use of MALDI-TOF MS

Evaluation of a real-time PCR assay for simultaneous detection of Kingella kingae and Staphylococcus aureus from synovial fluid in suspected septic arthritis

Direct plating of synovial fluid (SF) on agar-based media often fails to identify pathogens in septic arthritis (SA). We developed a PCR assay for the simultaneous detection of Kingella kingae and Staphylococcus aureus from SF to evaluate molecular detection in SF and to estimate the incidence of K. kingae in SA in North America. The assay was based on detection of the cpn60 gene of K. kingae and the spa gene of S. aureus in multiplex real-time PCR. K. kingae was identified in 50% of patients between 0 and 5 yr of age (n=6) but not in any patients >18 yr old (n=105). Direct plating of SF on agar-based media failed to detect K. kingae in all samples. The PCR assay was inferior to the culture-based method for S. aureus, detecting only 50% of culture-positive cases. Our findings suggest that K. kingae is a common pathogen in pediatric SA in North America, in agreement with previous reports from Europe. PCR-based assays for the detection of K. kingae may be considered in children with SA, especially in those with a high degree of clinical suspicion

Bridging the legitimacy gap—translating theory into practical signposts for legitimate flood risk governance

Legitimacy is widely regarded as a founding principle of ‘good’ and effective governance, yet despite intense academic debate and policy discourse, the concept remains conceptually confusing and poorly articulated in practice. To bridge this gap, this research performed an interpretive thematic analysis of academic scholarship across public administration, public policy, law, political science and geography. Three core themes were identified in relation to representative deliberation, procedural and distributive equity and justice, and socio-political acceptability, with numerous sub-themes therein. In an attempt to clarify conceptual confusion, this paper grounds these theoretical debates in the context of flood risk governance where numerous legitimacy dilemmas exist. A number of questions are presented as conceptual ‘sign posts’ to encourage reflexive governance in the future. Thus, more broadly, we assert the importance of bringing legitimacy to the forefront of contemporary flood risk governance discourse and practice, moving beyond the realm of academic reflection

Fundamental questions and applications of sclerochronology: Community-defined research priorities.

Horizon scanning is an increasingly common strategy to identify key research needs and frame future agendas in science. Here, we present the results of the first such exercise for the field of sclerochronology, thereby providing an overview of persistent and emergent research questions that should be addressed by future studies. Through online correspondence following the 5th International Sclerochronology Conference in 2019, participants submitted and rated questions that addressed either knowledge gaps or promising applications of sclerochronology. An initial list of 130 questions was compiled based on contributions of conference attendees and reviewed by expert panels formed during the conference. Herein, we present and discuss the 50 questions rated to be of the highest priority, determined through an online survey distributed to sclerochronology community members post the conference. The final list (1) includes important questions related to mechanisms of biological control over biomineralization, (2) highlights state of the art applications of sclerochronological methods and data for solving long-standing questions in other fields such as climate science and ecology, and (3) emphasizesthe need for common standards for data management and analysis. Although research priorities are continually reassessed, our list provides a roadmap that can be used to motivate research efforts and advance sclerochronology towardnew, and more powerful, applications.N/

2017 Research & Innovation Day Program

A one day showcase of applied research, social innovation, scholarship projects and activities.https://first.fanshawec.ca/cri_cripublications/1004/thumbnail.jp

Fundamental questions and applications of sclerochronology: Community-defined research priorities

Horizon scanning is an increasingly common strategy to identify key research needs and frame future agendas in science. Here, we present the results of the first such exercise for the field of sclerochronology, thereby providing an overview of persistent and emergent research questions that should be addressed by future studies. Through online correspondence following the 5th International Sclerochronology Conference in 2019, participants submitted and rated questions that addressed either knowledge gaps or promising applications of sclerochronology. An initial list of 130 questions was compiled based on contributions of conference attendees and reviewed by expert panels formed during the conference. Herein, we present and discuss the 50 questions rated to be of the highest priority, determined through an online survey distributed to sclerochronology community members post the conference. The final list: (1) includes important questions related to mechanisms of biological control over biomineralization; (2) highlights state of the art applications of sclerochronological methods and data for solving long-standing questions in other fields such as climate science and ecology: and (3) emphasizes the need for common standards for data management and analysis. Although research priorities are continually reassessed, our list provides a roadmap that can be used to motivate research efforts and advance sclerochronology toward new, and more powerful, applications

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