The effect of genomic information on optimal contribution selection in livestock breeding programs

BACKGROUND: Long-term benefits in animal breeding programs require that increases in genetic merit be balanced with the need to maintain diversity (lost due to inbreeding). This can be achieved by using optimal contribution selection. The availability of high-density DNA marker information enables the incorporation of genomic data into optimal contribution selection but this raises the question about how this information affects the balance between genetic merit and diversity. METHODS: The effect of using genomic information in optimal contribution selection was examined based on simulated and real data on dairy bulls. We compared the genetic merit of selected animals at various levels of co-ancestry restrictions when using estimated breeding values based on parent average, genomic or progeny test information. Furthermore, we estimated the proportion of variation in estimated breeding values that is due to within-family differences. RESULTS: Optimal selection on genomic estimated breeding values increased genetic gain. Genetic merit was further increased using genomic rather than pedigree-based measures of co-ancestry under an inbreeding restriction policy. Using genomic instead of pedigree relationships to restrict inbreeding had a significant effect only when the population consisted of many large full-sib families; with a half-sib family structure, no difference was observed. In real data from dairy bulls, optimal contribution selection based on genomic estimated breeding values allowed for additional improvements in genetic merit at low to moderate inbreeding levels. Genomic estimated breeding values were more accurate and showed more within-family variation than parent average breeding values; for genomic estimated breeding values, 30 to 40% of the variation was due to within-family differences. Finally, there was no difference between constraining inbreeding via pedigree or genomic relationships in the real data. CONCLUSIONS: The use of genomic estimated breeding values increased genetic gain in optimal contribution selection. Genomic estimated breeding values were more accurate and showed more within-family variation, which led to higher genetic gains for the same restriction on inbreeding. Using genomic relationships to restrict inbreeding provided no additional gain, except in the case of very large full-sib families

Streams of data from drops of water: 21st century molecular microbial ecology

Microorganisms are ubiquitous and represent a taxonomically and functionally diverse component of freshwater environments of significant ecological importance. The bacteria, archaea, and microbial eukarya in freshwater systems support a range of ecosystem processes and functions, including mediating all major biogeochemical cycles, and therefore regulate the flow of multiple ecosystem services. Yet relative to conspicuous higher taxa, microbial ecology remains poorly understood. As the anthropocene progresses, the demand for freshwater–ecosystem services is both increasing with growing human population density, and by association, increasingly threatened from multiple and often interacting stressors, such as climate change, eutrophication, and chemical pollution. Thus, it is imperative to understand the ecology of microorganisms and their functional role in freshwater ecosystems if we are to manage the future of these environments effectively. To do this, researchers have developed a vast array of molecular tools that can illuminate the diversity, composition, and activity of microbial communities. Within this primer, we discuss the history of molecular approaches in microbial ecology, and highlight the scope of questions that these methods enable researchers to address. Using some recent case studies, we describe some exemplar research into the microbial ecology of freshwater systems, and emphasize how molecular methods can provide novel ecological insights. Finally, we detail some promising developments within this research field, and how these might shape the future research landscape of freshwater microbial ecology

The filtering equations revisited

The problem of nonlinear filtering has engendered a surprising number of mathematical techniques for its treatment. A notable example is the change-of--probability-measure method originally introduced by Kallianpur and Striebel to derive the filtering equations and the Bayes-like formula that bears their names. More recent work, however, has generally preferred other methods. In this paper, we reconsider the change-of-measure approach to the derivation of the filtering equations and show that many of the technical conditions present in previous work can be relaxed. The filtering equations are established for general Markov signal processes that can be described by a martingale-problem formulation. Two specific applications are treated

An alternative approach to contrast-enhanced imaging: diffusion-weighted imaging and T1-weighted imaging identifies and quantifies necrosis in Wilms tumour

OBJECTIVES: Volume of necrosis in Wilms tumour is informative of chemotherapy response. Contrast-enhanced T1-weighted MRI (T1w) provides a measure of necrosis using gadolinium. This study aimed to develop a non-invasive method of identifying non-enhancing (necrotic) tissue in Wilms tumour. METHODS: In this single centre, retrospective study, post-chemotherapy MRI data from 34 Wilms tumour patients were reviewed (March 2012-March 2017). Cases with multiple b value diffusion-weighted imaging (DWI) and T1w imaging pre- and post-gadolinium were included. Fractional T1 enhancement maps were generated from the gadolinium T1w data. Multiple linear regression determined whether fitted parameters from a mono-exponential model (ADC) and bi-exponential model (IVIM - intravoxel incoherent motion) (D, D*, f) could predict fractional T1 enhancement in Wilms tumours, using normalised pre-gadolinium T1w (T1wnorm) signal as an additional predictor. Measured and predicted fractional enhancement values were compared using the Bland-Altman plot. An optimum threshold for separating necrotic and viable tissue using fractional T1 enhancement was established using ROC. RESULTS: ADC and D (diffusion coefficient) provided the strongest predictors of fractional T1 enhancement in tumour tissue (p < 0.001). Using the ADC-T1wnorm model (adjusted R2 = 0.4), little bias (mean difference = - 0.093, 95% confidence interval = [- 0.52, 0.34]) was shown between predicted and measured values of fractional enhancement and analysed via the Bland-Altman plot. The optimal threshold for differentiating viable and necrotic tissue was 33% fractional T1 enhancement (based on measured values, AUC = 0.93; sensitivity = 85%; specificity = 90%). CONCLUSIONS: Combining ADC and T1w imaging predicts enhancement in Wilms tumours and reliably identifies and measures necrotic tissue without gadolinium. KEY POINTS: • Alternative method to identify necrotic tissue in Wilms tumour without using contrast agents but rather using diffusion and T 1 weighted MRI. • A method is presented to visualise and quantify necrotic tissue in Wilms tumour without contrast. • The proposed method has the potential to reduce costs and burden to Wilms tumour patients who undergo longitudinal follow-up imaging as contrast agents are not used

A randomized trial to evaluate e-learning interventions designed to improve learner's performance, satisfaction, and self-efficacy with the AGREE II

<p>Abstract</p> <p>Background</p> <p>Practice guidelines (PGs) are systematically developed statements intended to assist in patient, practitioner, and policy decisions. The AGREE II is the revised and updated standard tool for guideline development, reporting and evaluation. It is comprised of 23 items and a user's Manual. The AGREE II is ready for use.</p> <p>Objectives</p> <p>To develop, execute, and evaluate the impact of two internet-based educational interventions designed to accelerate the capacity of stakeholders to use the AGREE II: a multimedia didactic tutorial with a virtual coach, and a higher intensity training program including both the didactic tutorial and an interactive practice exercise component.</p> <p>Methods</p> <p>Participants (clinicians, developers, and policy makers) will be randomly assigned to one of three conditions. <it>Condition one, didactic tutorial </it>-- participants will go through the on-line AGREE II tutorial supported by a virtual coach and review of the AGREE II prior to appraising the test PG. <it>Condition two, tutorial + practice </it>-- following the multimedia didactic tutorial with a virtual coach, participants will review the on-line AGREE II independently and use it to appraise a practice PG. Upon entering their AGREE II score for the practice PG, participants will be given immediate feedback on how their score compares to expert norms. If their score falls outside a predefined range, the participant will receive a series of hints to guide the appraisal process. Participants will receive an overall summary of their performance appraising the PG compared to expert norms. <it>Condition three, control arm </it>-- participants will receive a PDF copy of the AGREE II for review and to appraise the test PG on-line. All participants will then rate one of ten test PGs with the AGREE II. The outcomes of interest are learners' performance, satisfaction, self-efficacy, mental effort, and time-on-task; comparisons will be made across each of the test groups.</p> <p>Discussion</p> <p>Our research will test innovative educational interventions of various intensities and instructional design to promote the adoption of AGREE II and to identify those strategies that are most effective for training. The results will facilitate international capacity to apply the AGREE II accurately and with confidence and to enhance the overall guideline enterprise.</p

The N-terminal intrinsically disordered domain of mgm101p is localized to the mitochondrial nucleoid.

The mitochondrial genome maintenance gene, MGM101, is essential for yeasts that depend on mitochondrial DNA replication. Previously, in Saccharomyces cerevisiae, it has been found that the carboxy-terminal two-thirds of Mgm101p has a functional core. Furthermore, there is a high level of amino acid sequence conservation in this region from widely diverse species. By contrast, the amino-terminal region, that is also essential for function, does not have recognizable conservation. Using a bioinformatic approach we find that the functional core from yeast and a corresponding region of Mgm101p from the coral Acropora millepora have an ordered structure, while the N-terminal domains of sequences from yeast and coral are predicted to be disordered. To examine whether ordered and disordered domains of Mgm101p have specific or general functions we made chimeric proteins from yeast and coral by swapping the two regions. We find, by an in vivo assay in S.cerevisiae, that the ordered domain of A.millepora can functionally replace the yeast core region but the disordered domain of the coral protein cannot substitute for its yeast counterpart. Mgm101p is found in the mitochondrial nucleoid along with enzymes and proteins involved in mtDNA replication. By attaching green fluorescent protein to the N-terminal disordered domain of yeast Mgm101p we find that GFP is still directed to the mitochondrial nucleoid where full-length Mgm101p-GFP is targeted

The effects of weather and climate change on dengue

There is much uncertainty about the future impact of climate change on vector-borne diseases. Such uncertainty reflects the difficulties in modelling the complex interactions between disease, climatic and socioeconomic determinants. We used a comprehensive panel dataset from Mexico covering 23 years of province-specific dengue reports across nine climatic regions to estimate the impact of weather on dengue, accounting for the effects of non-climatic factors

Assessing Internet addiction using the parsimonious Internet addiction components model - a preliminary study [forthcoming]

Internet usage has grown exponentially over the last decade. Research indicates that excessive Internet use can lead to symptoms associated with addiction. To date, assessment of potential Internet addiction has varied regarding populations studied and instruments used, making reliable prevalence estimations difficult. To overcome the present problems a preliminary study was conducted testing a parsimonious Internet addiction components model based on Griffiths’ addiction components (2005), including salience, mood modification, tolerance, withdrawal, conflict, and relapse. Two validated measures of Internet addiction were used (Compulsive Internet Use Scale [CIUS], Meerkerk et al., 2009, and Assessment for Internet and Computer Game Addiction Scale [AICA-S], Beutel et al., 2010) in two independent samples (ns = 3,105 and 2,257). The fit of the model was analysed using Confirmatory Factor Analysis. Results indicate that the Internet addiction components model fits the data in both samples well. The two sample/two instrument approach provides converging evidence concerning the degree to which the components model can organize the self-reported behavioural components of Internet addiction. Recommendations for future research include a more detailed assessment of tolerance as addiction component

E-learning interventions are comparable to user's manual in a randomized trial of training strategies for the AGREE II

<p>Abstract</p> <p>Background</p> <p>Practice guidelines (PGs) are systematically developed statements intended to assist in patient and practitioner decisions. The AGREE II is the revised tool for PG development, reporting, and evaluation, comprised of 23 items, two global rating scores, and a new User's Manual. In this study, we sought to develop, execute, and evaluate the impact of two internet interventions designed to accelerate the capacity of stakeholders to use the AGREE II.</p> <p>Methods</p> <p>Participants were randomized to one of three training conditions. 'Tutorial'--participants proceeded through the online tutorial with a virtual coach and reviewed a PDF copy of the AGREE II. 'Tutorial + Practice Exercise'--in addition to the Tutorial, participants also appraised a 'practice' PG. For the practice PG appraisal, participants received feedback on how their scores compared to expert norms and formative feedback if scores fell outside the predefined range. <it>'</it>AGREE II User's Manual PDF (control condition)'<it>--</it>participants reviewed a PDF copy of the AGREE II only. All participants evaluated a test PG using the AGREE II. Outcomes of interest were learners' performance, satisfaction, self-efficacy, mental effort, time-on-task, and perceptions of AGREE II.</p> <p>Results</p> <p>No differences emerged between training conditions on any of the outcome measures.</p> <p>Conclusions</p> <p>We believe these results can be explained by better than anticipated performance of the AGREE II PDF materials (control condition) or the participants' level of health methodology and PG experience rather than the failure of the online training interventions. Some data suggest the online tools may be useful for trainees new to this field; however, this requires further study.</p