Introducing SPeDE : high-throughput dereplication and accurate determination of microbial diversity from matrix-assisted laser desorption-ionization time of flight mass spectrometry data

The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDE. IMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns

Sequence determinants of nucleotide binding in Sucrose Synthase : improving the affinity of a bacterial Sucrose Synthase for UDP by introducing plant residues

Sucrose Synthase (SuSy) catalyzes the reversible conversion of sucrose and a nucleoside diphosphate (NDP) into NDP-glucose and fructose. Biochemical characterization of several plant and bacterial SuSys has revealed that the eukaryotic enzymes preferentially use UDP whereas prokaryotic SuSys prefer ADP as acceptor. In this study, SuSy from the bacterium Acidithiobacillus caldus, which has a higher affinity for ADP as reflected by the 25-fold lower K-m value compared to UDP, was used as a test case to scrutinize the effect of introducing plant residues at positions in a putative nucleotide binding motif surrounding the nucleobase ring of NDP. All eight single to sextuple mutants had similar activities as the wild-type enzyme but significantly reduced K-m values for UDP (up to 60 times). In addition, we recognized that substrate inhibition by UDP is introduced by a methionine at position 637. The affinity for ADP also increased for all but one variant, although the improvement was much smaller compared to UDP. Further characterization of a double mutant also revealed more than 2-fold reduction in K-m values for CDP and GDP. This demonstrates the general impact of the motif on nucleotide binding. Furthermore, this research also led to the establishment of a bacterial SuSy variant that is suitable for the recycling of UDP during glycosylation reactions. The latter was successfully demonstrated by combining this variant with a glycosyltransferase in a one-pot reaction for the production of the C-glucoside nothofagin, a health-promoting flavonoid naturally found in rooibos (tea)

Developing mental health literacy and cultural competence in elite sport

Mental well-being, and mental health symptoms and disorders amongst elite athletes, have attracted a great deal of discussion recently. Current epidemiological evidence illustrates that mental health symptoms and disorders in elite athletes are prevalent and a concern for athletes, coaches, and sport organizations. Within the last two years, five consensus, expert, and position statements have been written on the topic of mental health in elite sport. A strategy suggested by each of the five statements and aimed at preventing and treating mental health symptoms and disorders in elite athletes, both individually and systemically, is, to employ education interventions, specifically those based on increasing mental health literacy. Mental health literacy has come to include concepts related to knowledge of effective self help and self-management strategies, challenging mental disorder stigma, awareness and use of mental health first aid to assist others, and the facilitation of help seeking behaviors. In elite sport, questions remain about how mental health literacy can address the unique needs of the individual athlete, but also factor in their culture and their environment in an effort to prevent and treat mental health symptoms and disorders. The purpose of this commentary is twofold: 1) to explore the evolving concept of mental health literacy within elite sport which addresses individuals, their culture, and their environment, and 2) to propose strategies for best practice and research in mental health literacy within elite sport relying on collaboration between sports psychiatry, sport psychology, and clinical psychology

A live-online mindfulness-based intervention for children living with epilepsy and their families: protocol for a randomized controlled trial of Making Mindfulness Matter©.

BACKGROUND: Epilepsy extends far beyond seizures; up to 80% of children with epilepsy (CWE) may have comorbid cognitive or mental health problems, and up to 50% of parents of CWE are at risk for major depression. Past research has also shown that family environment has a greater influence on children\u27s and parents\u27 health-related quality of life (HRQOL) and mental health than epilepsy-related factors. There is a pressing need for low-cost, innovative interventions to improve HRQOL and mental health for CWE and their parents. The aim of this randomized controlled trial (RCT) is to evaluate whether an interactive online mindfulness-based intervention program, Making Mindfulness Matter (M3), can be feasibly implemented and whether it positively affects CWE\u27s and parents\u27 HRQOL and mental health (specifically, stress, behavioral, depressive, and anxiety symptoms). METHODS: This parallel RCT was planned to recruit 100 child-parent dyads to be randomized 1:1 to the 8-week intervention or waitlist control and followed over 20 weeks. The intervention, M3, will be delivered online and separately to parents and children (ages 4-10 years) in groups of 4-8 by non-clinician staff of a local community epilepsy agency. The intervention incorporates mindful awareness, social-emotional learning skills, and positive psychology. It is modeled after the validated school-based MindUP program and adapted for provision online and to include a parent component. DISCUSSION: This RCT will determine whether this online mindfulness-based intervention is feasible and effective for CWE and their parents. The proposed intervention may be an ideal vector to significantly improve HRQOL and mental health for CWE and their parents given its low cost and implementation by community epilepsy agencies. TRIAL REGISTRATION: ClinicalTrials.gov NCT04020484 . Registered on July 16, 2019

Young people today: news media, policy and youth justice

The new sociology of childhood sees children as competent social agents with important contributions to make. And yet the phase of childhood is fraught with tensions and contradictions. Public policies are required, not only to protect children, but also to control them and regulate their behaviour. For children and young people in the UK, youth justice has become increasingly punitive. At the same time, social policies have focused more on children's inclusion and participation. In this interplay of conflict and contradictions, the role the media play is critical in contributing to the moral panic about childhood and youth. In this article, we consider media representations of “antisocial” children and young people and how this belies a moral response to the nature of contemporary childhood. We conclude by considering how a rights-based approach might help redress the moralised politics of childhood representations in the media

The First Provenance Challenge

The first Provenance Challenge was set up in order to provide a forum for the community to help understand the capabilities of different provenance systems and the expressiveness of their provenance representations. To this end, a Functional Magnetic Resonance Imaging workflow was defined, which participants had to either simulate or run in order to produce some provenance representation, from which a set of identified queries had to be implemented and executed. Sixteen teams responded to the challenge, and submitted their inputs. In this paper, we present the challenge workflow and queries, and summarise the participants contributions

Attitudes and Performance: An Analysis of Russian Workers

This paper investigates the relationship between locus of control and performance among Russian employees, using survey data collected at 28 workplaces in 2002 in Taganrog and at 47 workplaces in 2003 in Ekaterinburg. We develop a measure that allows us to categorize the Russian employees participating in our survey as exhibiting an internal or external locus of control. We then assess the extent to which there are significant differences between “internals” and “externals” in work-related attitudes that may affect performance. In particular, we focus on (1) attitudes about outcomes associated with hard work, (2) level of job satisfaction, (3) expectation of receiving a desired reward, and (4) loyalty to and involvement with one’s organization. In each case we identify where gender and generational differences emerge. Our main objective is to determine whether Russian employees who exhibit an internal locus of control perform better than employees with an external locus of control. Our performance measures include earnings, expected promotions, and assessments of the quantity and quality of work in comparison to others at the same organization doing a similar job. Controlling for a variety of worker characteristics, we find that (1) individuals who exhibit an internal locus of control perform better, but this result is not always statistically significant; (2) even among “internals,” women earn significantly less than men and have a much lower expectation of promotion; (3) even among “internals,” experience with unemployment has a negative influence on performance.http://deepblue.lib.umich.edu/bitstream/2027.42/40144/3/wp758.pd

Just-in-Time Information Improved Decision-Making in Primary Care: A Randomized Controlled Trial

BACKGROUND: The "Just-in-time Information" (JIT) librarian consultation service was designed to provide rapid information to answer primary care clinical questions during patient hours. This study evaluated whether information provided by librarians to answer clinical questions positively impacted time, decision-making, cost savings and satisfaction. METHODS AND FINDING: A randomized controlled trial (RCT) was conducted between October 2005 and April 2006. A total of 1,889 questions were sent to the service by 88 participants. The object of the randomization was a clinical question. Each participant had clinical questions randomly allocated to both intervention (librarian information) and control (no librarian information) groups. Participants were trained to send clinical questions via a hand-held device. The impact of the information provided by the service (or not provided by the service), additional resources and time required for both groups was assessed using a survey sent 24 hours after a question was submitted. The average time for JIT librarians to respond to all questions was 13.68 minutes/question (95% CI, 13.38 to 13.98). The average time for participants to respond their control questions was 20.29 minutes/question (95% CI, 18.72 to 21.86). Using an impact assessment scale rating cognitive impact, participants rated 62.9% of information provided to intervention group questions as having a highly positive cognitive impact. They rated 14.8% of their own answers to control question as having a highly positive cognitive impact, 44.9% has having a negative cognitive impact, and 24.8% with no cognitive impact at all. In an exit survey measuring satisfaction, 86% (62/72 responses) of participants scored the service as having a positive impact on care and 72% (52/72) indicated that they would use the service frequently if it were continued. CONCLUSIONS: In this study, providing timely information to clinical questions had a highly positive impact on decision-making and a high approval rating from participants. Using a librarian to respond to clinical questions may allow primary care professionals to have more time in their day, thus potentially increasing patient access to care. Such services may reduce costs through decreasing the need for referrals, further tests, and other courses of action. TRIAL REGISTRATION: Controlled-Trials.com ISRCTN96823810