Using genotyping-by-sequencing to understand Musa diversity

Poster presented at Plant and Animal Genome, PAG XXII. San Diego (USA), 11-15 Jan 201

A Novel Approach to Multimedia Ontology Engineering for Automated Reasoning over Audiovisual LOD Datasets

Multimedia reasoning, which is suitable for, among others, multimedia content analysis and high-level video scene interpretation, relies on the formal and comprehensive conceptualization of the represented knowledge domain. However, most multimedia ontologies are not exhaustive in terms of role definitions, and do not incorporate complex role inclusions and role interdependencies. In fact, most multimedia ontologies do not have a role box at all, and implement only a basic subset of the available logical constructors. Consequently, their application in multimedia reasoning is limited. To address the above issues, VidOnt, the very first multimedia ontology with SROIQ(D) expressivity and a DL-safe ruleset has been introduced for next-generation multimedia reasoning. In contrast to the common practice, the formal grounding has been set in one of the most expressive description logics, and the ontology validated with industry-leading reasoners, namely HermiT and FaCT++. This paper also presents best practices for developing multimedia ontologies, based on my ontology engineering approach

A systematic review of shared decision making interventions in child and youth mental health: synthesising the use of theory, intervention functions, and behaviour change techniques

Reviews around interventions to improve shared decision making (SDM) for child and youth mental health have produced inconclusive findings on what approaches increase participation. Importantly, the previous reviews did not explore the use of theory, as well as mechanisms of change (intervention functions) and active units of change (behaviour change techniques). The aim of this review was to explore these factors and ascertain how, if at all, these contribute to SDM. Five databases were searched up until April 2020. Studies met inclusion criteria if they were: (a) an intervention to facilitate SDM; (b) aimed at children, adolescence, or young people aged up to 25, with a mental health difficulty, or their parents/guardians; and (c) included a control group. Data were extracted on patient characteristics, study design, intervention, theoretical background, intervention functions, behaviour change techniques, and SDM. Quality assessment of the studies was undertaken using the Effective Public Health Practice Project (EPHPP) quality assessment tool. Eight different interventions met inclusion criteria. The role of theory to increase SDM remains unclear. Specific intervention functions, such as 'education' on SDM and treatment options and 'environmental restructuring' using decision aids, are being used in SDM interventions, as well as 'training' for clinicians. Similarly, behaviour change techniques linked to these, such as 'adding objects to the environment', 'discussing pros/cons', and clinicians engaging in 'behavioural practice/rehearsal'. However, as most studies scored low on the quality assessment criteria, as well as a small number of studies included and a low number of behaviour change techniques utilised, links between behaviour change techniques, intervention functions and increased participation remain tentative. Intervention developers and clinicians may wish to consider specific intervention functions and behaviour change techniques to facilitate SDM

Predictors of Clostridium Difficile Colitis Infections in Hospitals.

Hospital-level predictors of high rates of \u27Clostridium difficile-associated disease\u27 (CDAD) were evaluated in over 2300 hospitals across California, Arizona, and Minnesota. American Hospital Association data were used to determine hospital characteristics associated with high rates of CDAD. Significant correlations were found between hospital rates of CDAD, common infections and other identified pathogens. Hospitals in urban areas had higher average rates of CDAD; yet, irrespective of geographic location, hospital rates of CDAD were associated with other infections. In addition, hospitals with \u27high CDAD\u27 rates had slower turnover of beds and were more likely to offer transplant services. These results reveal large differences in rates of CDAD across regions. Hospitals with high rates of CDAD have high rates of other common infections, suggesting a need for broad infection control policies

What is Normalization? The Strategies Employed in Top-Down and Bottom-Up Proteome Analysis Workflows.

The accurate quantification of changes in the abundance of proteins is one of the main applications of proteomics. The maintenance of accuracy can be affected by bias and error that can occur at many points in the experimental process, and normalization strategies are crucial to attempt to overcome this bias and return the sample to its regular biological condition, or normal state. Much work has been published on performing normalization on data post-acquisition with many algorithms and statistical processes available. However, there are many other sources of bias that can occur during experimental design and sample handling that are currently unaddressed. This article aims to cast light on the potential sources of bias and where normalization could be applied to return the sample to its normal state. Throughout we suggest solutions where possible but, in some cases, solutions are not available. Thus, we see this article as a starting point for discussion of the definition of and the issues surrounding the concept of normalization as it applies to the proteomic analysis of biological samples. Specifically, we discuss a wide range of different normalization techniques that can occur at each stage of the sample preparation and analysis process

Estimating gonorrhoea prevalence in young heterosexual men and women attending community-based sexual health services to inform decisions on gonorrhoea testing.

In England, dual tests detecting chlamydia and gonorrhoea are used in specialist and community-based sexual health services (SHSs). Test performance is poor when prevalence is low, therefore UK national guidelines recommend against opportunistic gonorrhoea screening unless there is a clear local public health need. While surveillance data on gonorrhoea prevalence is comprehensive in specialist SHSs, it is sparse in community SHSs. We aimed to estimate gonorrhoea prevalence in heterosexual men and women aged 15-24 attending community SHSs to inform testing care pathways. We used linear and quadratic regression to model the relationship between prevalence in community and specialist SHSs in local authorities (LAs) with available surveillance data. We applied best-fitting models to predict prevalence in community SHSs in remaining LAs. Data from community SHSs were available for 102/326 LAs. There was a weak positive association between gonorrhoea prevalence in community and specialist SHSs in corresponding LAs within (R 2 = 0·13, P = 0·058) and outside (R 2 = 0·07, P = 0·02) London. Applying best-fitting models, we estimated a median gonorrhoea prevalence of 0·5% (mean 0·6%; range 0·2%-2·7%) in heterosexuals attending community SHSs. Despite some unexplained variation, our analyses suggest gonorrhoea prevalence in young heterosexuals attending community SHSs is below 1% in most English LAs. Our findings re-inforce the current national guidelines that recommend care pathways for gonorrhoea testing in community SHSs include confirmatory testing to reduce the risk of misdiagnosis and inappropriate management

Continuous-wave versus pulse regime in a passively mode-locked laser with a fast saturable absorber

The phenomenon of modulation instability of continuous-wave (cw) solutions of the cubic-quintic complex Ginzburg-Landau equation is studied. It is shown that low-amplitude cw solutions are always unstable. For higher-amplitude cw solutions, there are regions of stability and regions where the cw solutions are modulationally unstable. It is found that there is an indirect relation between the stability of the soliton solutions and the modulation instability of the higher-amplitude cw solutions. However, there is no one-to-one correspondence between the two. We show that the evolution of modulationally unstable cw's depends on the system parameters