Harbin: a quantitation PCR analysis tool

Objectives: To enable analysis and comparisons of different relative quantitation experiments, a web-browser application called Harbin was created that uses a quantile-based scoring system for the comparison of samples at different time points and between experiments. Results: Harbin uses the standard curve method for relative quantitation to calculate concentration ratios (CRs). To evaluate if different datasets can be combined the Harbin quantile bootstrap test is proposed. This test is more sensitive in detecting distributional differences between data sets than the Kolmogorov–Smirnov test. The utility of the test is demonstrated in a comparison of three grapevine leafroll associated virus 3 (GLRaV-3) RT-qPCR data sets. Conclusions: The quantile-based scoring system of CRs will enable the monitoring of virus titre or gene expression over different time points and be useful in other genomic applications where the combining of data sets are required

The diagnostic patterns of the iso-enitmes of serum non-specific alkaline phosphatase

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Knowledge mobilization: stepping into interdependent and relational space using co-creation

In recent years, there has been a growing interest in using co-creation approaches, with academics and partners working together to create research and interventions to achieve impact. Action research typically starts with the question ‘how can we improve this situation?’ and then co-creates knowledge with and not on or for people. This approach contrasts with conventional approaches in which academics create knowledge and then disseminate it to users via conferences, reports etc. The co-creative approach involves a shift in academics’ thinking and approaches. The success of co-creation depends on the academic shifting from being self-focussed and independent to being other-focussed and interdependent. In this paper, we outline the theoretical background that has informed our thinking and practices related to knowledge mobilization, and our novel relational approach. We illustrate our approach using two co-created projects, focused on enhancing early literacy and supporting mothers with substance use problems. We hope that this will help others consider when it may be appropriate to use a co-creative approach and how to engage in this co-creation process, including awareness of common barriers and benefits

The Co-produced Pathway to Impact Describes Knowledge Mobilization Processes

Knowledge mobilization supports research collaborations between university and community partners which can maximize the impacts of research beyond the academy; however, models of knowledge mobilization are complex and create challenges for monitoring research impacts. This inability to sufficiently evaluate is particularly problematic for large collaborative research networks involving multiple partners and research institutions. The Co-produced Pathway to Impact simplifies many of the complex models of knowledge mobilization. It is a logic model based framework for mapping the progress of research -\u3e dissemination -\u3e uptake -\u3e implementation -\u3e impact. This framework is illustrated using collaborative research projects from Promoting Relationships and Eliminating Violence Network (PREVNet), a pan-Canadian community-university network engaging in knowledge mobilization to promote healthy relationships among children and youth and prevent bullying. The Co-produced Pathway to Impact illustrates that research impact occurs when university researchers collaborate with non-academic partners who produce the products, policies, and services that have impacts on the lives of end beneficiaries. Research impact is therefore measured at the level of non-academic partners and identified by surveying research partners to create narrative case studies of research impact

Multi-species temporal network of livestock movements for disease spread

Introduction: The objective of this study is to show the importance of interspecies links and temporal network dynamics of a multi-species livestock movement network. Although both cattle and sheep networks have been previously studied, cattle-sheep multi-species networks have not generally been studied in-depth. The central question of this study is how the combination of cattle and sheep movements affects the potential for disease spread on the combined network. Materials and methods: Our analysis considers static and temporal representations of networks based on recorded animal movements. We computed network-based node importance measures of two single-species networks, and compared the top-ranked premises with the ones in the multi-species network. We propose the use of a measure based on contact chains calculated in a network weighted with transmission probabilities to assess the importance of premises in an outbreak. To ground our investigation in infectious disease epidemiology, we compared this suggested measure with the results of disease simulation models with asymmetric probabilities of transmission between species. Results: Our analysis of the temporal networks shows that the premises which are likely to drive the epidemic in this multi-species network differ from the ones in both the cattle and the sheep networks. Although sheep movements are highly seasonal, the estimated size of an epidemic is significantly larger in the multi-species network than in the cattle network, independently of the period of the year. Finally, we demonstrate that a measure based on contact chains allow us to identify around 30% of the key farms in a simulated epidemic, ignoring markets, whilst static network measures identify less than 10% of these farms. Conclusion: Our results ascertain the importance of combining species networks, as well as considering layers of temporal livestock movements in detail for the study of disease spread

Storing and manipulating environmental big data with JASMIN

JASMIN is a super-data-cluster designed to provide a high-performance high-volume data analysis environment for the UK environmental science community. Thus far JASMIN has been used primarily by the atmospheric science and earth observation communities, both to support their direct scientific workflow, and the curation of data products in the STFC Centre for Environmental Data Archival (CEDA). Initial JASMIN configuration and first experiences are reported here. Useful improvements in scientific workflow are presented. It is clear from the explosive growth in stored data and use that there was a pent up demand for a suitable big-data analysis environment. This demand is not yet satisfied, in part because JASMIN does not yet have enough compute, the storage is fully allocated, and not all software needs are met. Plans to address these constraints are introduced

“I h 8 u”: Findings from a five-year study of text and e-mail bullying

Copyright @ 2010 British Educational Research Association. The final version of this article is available at the link below.This study charts reports of nasty or threatening text and e-mail messages received by students in academic years 7 and 8 (11-13 years of age) attending 13 secondary schools in the North of England between 2002-2006. Annual surveys were undertaken on behalf of the local education authority (LEA) to monitor bullying. Results indicated that, over five years, the number of pupils receiving one or more nasty or threatening text messages or e-mails increased significantly, particularly among girls. However, receipt of frequent nasty or threatening text and e-mail messages remained relatively stable. For boys, being a victim of direct-physical bullying was associated with receiving nasty or threatening text and e-mail messages; for girls it was being unpopular among peers. Boys received more hate-related messages and girls were primarily the victims of name-calling, Findings are discussed with respect to theoretical and policy developments, and recommendations for future research are offered

Young adult outcomes associated with teen pregnancy among high-risk girls in a randomized controlled trial of Multidimensional Treatment Foster Care

Teen pregnancy is associated with a host of deleterious outcomes for girls, such as drug use and poor parenting. Thus, reducing teen pregnancy rates could improve long-term developmental outcomes for girls, including adjustment during young adulthood. Based on the positive effects of Multidimensional Treatment Foster Care (MTFC) relative to group care (GC) in a study of adolescent girls (significantly fewer pregnancies reported in the 2-year follow-up for MTFC girls), the present study followed this sample into young adulthood (approximately 7 years post-baseline) to examine the effects of adolescent pregnancy on young adult substance use and pregnancy-related outcomes. All participants were randomly assigned to MTFC (N = 81) or GC (N = 85) as adolescents as part of a randomized controlled trial (RCT). Results from logistic regression analyses indicated that becoming pregnant during the 2-year follow-up was significantly related to illicit drug use, miscarriage from a new pregnancy, and child welfare involvement 7 years post-baseline. In addition, baseline marijuana use predicted marijuana use at 7 years post-baseline. © 2013 Copyright Taylor and Francis Group, LLC