Mapping Educational Specialist knowHow (MESH): the building of a knowledge management system for research informed practice

In this invited article the authors present an evaluative report on the development of the MESHGuides project (http://www.meshguides.org/). MESHGuides’ objective is to provide education with an international knowledge management system. MESHGuides were conceived as research summaries for supporting teachers’ in developing evidence-based practice. Their aim is to enhance teachers’ capacity to engage actively with research in their own classrooms. The original thinking for MESH arose from the work of UK-based academics Professor Marilyn Leask and Dr Sarah Younie in response to a desire, which has recently gathered momentum in the UK, for the development of a more research-informed teaching profession and for the establishment of an on-line platform to support evidence-based practice (DfE, 2015; Leask and Younie 2001; OECD 2009). The focus of this article is on how the MESHGuides project was conceived and structured, the technical systems supporting it and the practical reality for academics and teachers of composing and using MESHGuides. The project and the guides are in the early stages of development, and discussion indicates future possibilities for more global engagement with this knowledge management system.

Genetic dissection of heterosis using epistatic association mapping in a partial NCII mating design

Heterosis refers to the phenomenon in which an F1 hybrid exhibits enhanced growth or agronomic performance. However, previous theoretical studies on heterosis have been based on bi-parental segregating populations instead of F1 hybrids. To understand the genetic basis of heterosis, here we used a subset of F1 hybrids, named a partial North Carolina II design, to perform association mapping for dependent variables: original trait value, general combining ability (GCA), specific combining ability (SCA) and mid-parental heterosis (MPH). Our models jointly fitted all the additive, dominance and epistatic effects. The analyses resulted in several important findings: 1) Main components are additive and additive-by-additive effects for GCA and dominance-related effects for SCA and MPH, and additive-by-dominant effect for MPH was partly identified as additive effect; 2) the ranking of factors affecting heterosis was dominance > dominance-by-dominance > over-dominance > complete dominance; and 3) increasing the proportion of F1 hybrids in the population could significantly increase the power to detect dominance-related effects, and slightly reduce the power to detect additive and additive-by-additive effects. Analyses of cotton and rapeseed datasets showed that more additive-by-additive QTL were detected from GCA than from trait phenotype, and fewer QTL were from MPH than from other dependent variables.

An Ensemble Kalman Smoother for Nonlinear Dynamics

It is for mally proved that the general smoother for nonlinear dynamics can be for mulated as a sequential method, that is, obser vations can be assimilated sequentially during a for ward integration. The general filter can be derived from the smoother and it is shown that the general smoother and filter solutions at the final time become identical, as is expected from linear theor y. Then, a new smoother algorithm based on ensemble statistics is presented and examined in an example with the Lorenz equations. The new smoother can be computed as a sequential algorithm using only for ward-in-time model integrations. It bears a strong resemblance with the ensemble Kalman filter . The difference is that ever y time a new dataset is available during the for ward integration, an analysis is computed for all previous times up to this time. Thus, the first guess for the smoother is the ensemble Kalman filter solution, and the smoother estimate provides an improvement of this, as one would expect a smoother to do. The method is demonstrated in this paper in an intercomparison with the ensemble Kalman filter and the ensemble smoother introduced by van Leeuwen and Evensen, and it is shown to be superior in an application with the Lorenz equations. Finally , a discussion is given regarding the properties of the analysis schemes when strongly non-Gaussian distributions are used. It is shown that in these cases more sophisticated analysis schemes based on Bayesian statistics must be used.

A joint state and parameter estimation scheme for nonlinear dynamical systems

We present a novel algorithm for concurrent model state and parameter estimation in nonlinear dynamical systems. The new scheme uses ideas from three dimensional variational data assimilation (3D-Var) and the extended Kalman filter (EKF) together with the technique of state augmentation to estimate uncertain model parameters alongside the model state variables in a sequential filtering system. The method is relatively simple to implement and computationally inexpensive to run for large systems with relatively few parameters. We demonstrate the efficacy of the method via a series of identical twin experiments with three simple dynamical system models. The scheme is able to recover the parameter values to a good level of accuracy, even when observational data are noisy. We expect this new technique to be easily transferable to much larger models.

A new three-locus model for rootstock-induced dwarfing in apple revealed by genetic mapping of root bark percentage

Rootstock-induced dwarfing of apple scions revolutionized global apple production during the twentieth century, leading to the development of modern intensive orchards. A high root bark percentage (the percentage of the whole root area constituted by root cortex) has previously been associated with rootstock induced dwarfing in apple. In this study, the root bark percentage was measured in a full-sib family of ungrafted apple rootstocks and found to be under the control of three loci. Two QTL for root bark percentage were found to co-localise to the same genomic regions on chromosome 5 and chromosome 11 previously identified as controlling dwarfing, Dw1 and Dw2, respectively. A third QTL was identified on chromosome 13 in a region that has not been previously associated with dwarfing. The development of closely linked 3 Sequence-tagged site STS markers improved the resolution of allelic classes thereby allowing the detection of dominance and epistatic interactions between loci, with high root bark percentage only occurring in specific allelic combinations. In addition, we report a significant negative correlation between root bark percentage and stem diameter (an indicator of tree vigour), measured on a clonally propagated grafted subset of the mapping population. The demonstrated link between root bark percentage and rootstock-induced dwarfing of the scion leads us to propose a three-locus model that is able to explain levels of dwarfing from the dwarf ‘M.27’ to the semi-invigorating rootstock ‘M.116’. Moreover, we suggest that the QTL on chromosome 13 (Rb3) might be analogous to a third dwarfing QTL, Dw3 that has not previously been identified.

Anticipating future risk in social-ecological systems using fuzzy cognitive mapping: the case of wildfire in the Chiquitania, Bolivia

Understanding complex social-ecological systems, and anticipating how they may respond to rapid change, requires an approach that incorporates environmental, social, economic, and policy factors, usually in a context of fragmented data availability. We employed fuzzy cognitive mapping (FCM) to integrate these factors in the assessment of future wildfire risk in the Chiquitania region, Bolivia. In this region, dealing with wildfires is becoming increasingly challenging due to reinforcing feedbacks between multiple drivers. We conducted semi-structured interviews and constructed different FCMs in focus groups to understand the regional dynamics of wildfire from diverse perspectives. We used FCM modelling to evaluate possible adaptation scenarios in the context of future drier climatic conditions. Scenarios also considered possible failure to respond in time to the emergent risk. This approach proved of great potential to support decision-making for risk management. It helped identify key forcing variables and generate insights into potential risks and trade-offs of different strategies. All scenarios showed increased wildfire risk in the event of more droughts. The ‘Hands-off’ scenario resulted in amplified impacts driven by intensifying trends, affecting particularly the agricultural production. The ‘Fire management’ scenario, which adopted a bottom-up approach to improve controlled burning, showed less trade-offs between wildfire risk reduction and production compared to the ‘Fire suppression’ scenario. Findings highlighted the importance of considering strategies that involve all actors who use fire, and the need to nest these strategies for a more systemic approach to manage wildfire risk. The FCM model could be used as a decision-support tool and serve as a ‘boundary object’ to facilitate collaboration and integration of different forms of knowledge and perceptions of fire in the region. This approach has also the potential to support decisions in other dynamic frontier landscapes around the world that are facing increased risk of large wildfires.

Auriculo-condylar syndrome: mapping of a first locus and evidence for genetic heterogeneity

Auriculo-condylar syndrome (ACS), an autosomal dominant disorder of first and second pharyngeal arches, is characterized by malformed ears (`question mark ears`), prominent cheeks, microstomia, abnormal temporomandibular joint, and mandibular condyle hypoplasia. Penetrance seems to be complete, but there is high inter-and intra-familial phenotypic variation, with no evidence of genetic heterogeneity. We herein describe a new multigeneration family with 11 affected individuals (F1), in whom we confirm intra-familial clinical variability. Facial asymmetry, a clinical feature not highlighted in other ACS reports, was highly prevalent among the patients reported here. The gene responsible for ACS is still unknown and its identification will certainly contribute to the understanding of human craniofacial development. No chromosomal rearrangements have been associated with ACS, thus mapping and positional cloning is the best approach to identify this disease gene. To map the ACS gene, we conducted linkage analysis in two large ACS families, F1 and F2 (F2; reported elsewhere). Through segregation analysis, we first excluded three known loci associated with disorders of first and second pharyngeal arches (Treacher Collins syndrome, oculo-auriculo-vertebral spectrum, and Townes-Brocks syndrome). Next, we performed a wide genome search and we observed evidence of linkage to 1p21.1-q23.3 in F2 (LOD max 3.01 at theta = 0). Interestingly, this locus was not linked to the phenotype segregating in F1. Therefore, our results led to the mapping of a first locus of ACS (ACS1) and also showed evidence for genetic heterogeneity, suggesting that there are at least two loci responsible for this phenotype.