Ontological Levels in Histological Imaging

Paper presented at the 9th edition of the Formal Ontology in Information Systems conference, FOIS 2016, July 6–9, 2016, Annecy, FranceThis is the author accepted manuscript. The final version is available from IOS Press via the DOI in this record.In this paper we present an ontological perspective on ongoing work in histological and histopathological imaging involving the quantitative and algorithmic analysis of digitised images of cells and tissues. We present the derivation of consistent histological models from initially captured images of prepared tissue samples as a progression through a number of ontological levels, each populated by its distinctive classes of entities related in systematic ways to entities at other levels. We see this work as contributing to ongoing efforts to provide a consistent and widely accepted suite of ontological resources such as those currently constituting the OBO Foundry, and where possible we draw links between our work and existing ontologies within that suite.This research is supported by EPSRC through funding under grant EP/M023869/1 “Novel context-based segmentation algorithms for intelligent microscopy”

Automatic thresholding from the gradients of region boundaries

We present an approach for automatic threshold segmentation of greyscale images. The procedure is inspired by a reinterpretation of the strategy observed in human operators when adjusting thresholds manually and interactively by means of ‘slider’ controls. The approach translates into two methods. The first one is suitable for single or multiple global thresholds to be applied globally to images and consists of searching for a threshold value that generates a phase whose boundary coincides with the largest gradients in the original image. The second method is a variation, implemented to operate on the discrete connected components of the thresholded phase (i.e. the binary regions) independently. Consequently, this becomes an adaptive local threshold procedure, which operates relative to regions, rather than to local image subsets as is the case in most local thresholding methods previously published. Adding constraints for specifying certain classes of expected objects in the images can improve the output of the method over the traditional ‘segmenting first, then classify’ approach.The research reported in this paper was supported by the Engineering and Physical Sciences Research Council (EPSRC), UK through funding under grant EP/M023869/1 ‘Novel contextbased segmentation algorithms for intelligent microscopy’

Mining candidate causal relationships in movement patterns

This is an Accepted Manuscript of an article published by Taylor & Francis in the International Journal of Geographical Information Science on 01 October 2013, available online: http://wwww.tandfonline.com/10.1080/13658816.2013.841167In many applications, the environmental context for, and drivers of movement patterns are just as important as the patterns themselves. This paper adapts standard data mining techniques, combined with a foundational ontology of causation, with the objective of helping domain experts identify candidate causal relationships between movement patterns and their environmental context. In addition to data about movement and its dynamic environmental context, our approach requires as input definitions of the states and events of interest. The technique outputs causal and causal-like relationships of potential interest, along with associated measures of support and confidence. As a validation of our approach, the analysis is applied to real data about fish movement in the Murray River in Australia. The results demonstrate the technique is capable of identifying statistically significant patterns of movement indicative of causal and causal-like relationships. 1365-8816Australian Research Council Discovery Projec

Assessing the fidelity of delivery of an intervention to increase attendance at the English Stop Smoking Services

Background: Implementation fidelity refers to the extent to which a proposed intervention is enacted as designed and is necessary to determine how much the intervention in question is the primary mechanism in any changes observed. Start2quit was a randomised controlled trial that aimed to improve attendance at the English Stop Smoking Service (SSS). The complex intervention combining computer-tailored personal risk letters and no-commitment (“taster”) sessions aimed at encouraging attendance at the SSS doubled attendance at the SSS and significantly increased abstinence rates, although attendance and abstinence varied between participating SSSs. Assessment of the fidelity of the delivery of the taster sessions to the protocol was embedded into the trial and is the focus of this study. / Methods: Eighteen SSSs participated in the study. Taster sessions were delivered by SSS advisors in the area. Of the 131 sessions delivered, 93 (71 %) were recorded and 41 (31.3 %) were selected for transcription and analysis. The taster session protocol contained 73 specified behaviours, which were independently classified into component behaviour change techniques (BCTs) using an established taxonomy for smoking cessation. All transcripts were coded by two authors with 25 % additionally coded by a third. The fidelity of each taster session was expressed as the percentage of overall protocol-specified behaviours that were delivered. Adherence to each BCT was measured as the number of behaviours applied by the advisors within each BCT divided by the total number classified within each. / Results: Adherence of protocol-specified behaviours was relatively high (median 71.23 %), though there was considerable variation (28.76 to 95.89 %) in individual sessions. Median fidelity to specific BCTs across sessions also varied from 50 to 100 %. Shorter sessions, sessions run jointly by two advisors, by female advisors, or by advisors aged 45 to 54 were associated with higher levels of adherence. There was no association between adherence and subsequent attendance at the SSS. / Conclusions: These results suggest that the delivery of the intervention of this study is not likely to have been impacted by issues of fidelity. As such, we can have greater confidence that variability in the main outcome is not due to variability in SSS advisor adherence to the protocol of the taster sessions. / Trial registration: Current Controlled Trials ISRCTN7656191

Motivation in physical education across the primary-secondary school transition

The purpose of this study was to examine the temporal patterns of approach-avoidance achievement goals, implicit theories of ability and perceived competence in physical education across the transition from primary to secondary school. We also evaluated the predictive utility of implicit theories and perceived competence with regard to achievement goal adoption, and determined the moderating influence of gender on temporal patterns and antecedent–goal relationships. One hundred and forty pupils (mean age at start of study = 11.37 years, SD =.28) completed measures of entity and incremental beliefs, perceived competence and goals on four occasions during a 12-month period. Mastery-approach, performance-approach and perform-ance-avoidance goals, as well as entity and incremental beliefs, exhibited a linear decline over time. Mastery-avoidance goals showed no significant change. Girls exhibited a linear decline in perceived competence, whereas for boys the trajectory was curvilinear. Competence perceptions predicted initial scores, but not rate of change, on mastery-approach and both types of performance goals. Incrementa

Modeling interannual dense shelf water export in the region of the Mertz Glacier Tongue (1992-2007)

1] Ocean observations around the Australian-Antarctic basin show the importance of coastal latent heat polynyas near the Mertz Glacier Tongue (MGT) to the formation of Dense Shelf Water (DSW) and associated Antarctic Bottom Water (AABW). Here, we use a regional ocean/ice shelf model to investigate the interannual variability of the export of DSW from the Adélie (west of the MGT) and the Mertz (east of the MGT) depressions from 1992 to 2007. The variability in the model is driven by changes in observed surface heat and salt fluxes. The model simulates an annual mean export of DSW through the Adélie sill of about 0.07 ± 0.06 Sv. From 1992 to 1998, the export of DSW through the Adélie (Mertz) sills peaked at 0.14 Sv (0.29 Sv) during July to November. During periods of mean to strong polynya activity (defined by the surface ocean heat loss), DSW formed in the Adélie depression can spread into the Mertz depression via the cavity under the MGT. An additional simulation, where ocean/ice shelf thermodynamics have been disabled, highlights the fact that models without ocean/ice shelf interaction processes will significantly overestimate rates of DSW export. The melt rates of the MGT are 1.2 ± 0.4 m yr−1 during periods of average to strong polynya activity and can increase to 3.8 ± 1.5 m/yr during periods of sustained weak polynya activity, due to the increased presence of relatively warmer water interacting with the base of the ice shelf. The increased melting of the MGT during a weak polynya state can cause further freshening of the DSW and ultimately limits the production of AABW

Vertical Processes and Resolution Impact Ice Shelf Basal Melting: A Multi-Model Study

Understanding ice shelf–ocean interaction is fundamental to projecting the Antarctic ice sheet response to a warming climate. Numerical ice shelf–ocean models are a powerful tool for simulating this interaction, yet are limited by inherent model weaknesses and scarce observations, leading to parameterisations that are unverified and unvalidated below ice shelves. We explore how different models simulate ice shelf–ocean interaction using the 2nd Ice Shelf–Ocean Model Intercomparison Project (ISOMIP+) framework. Vertical discretisation and resolution of the ocean model are shown to have a significant effect on ice shelf basal melt rate, through differences in the distribution of meltwater fluxes and the calculation of thermal driving. Z-coordinate models, which generally have coarser vertical resolution in ice shelf cavities, may simulate higher melt rates compared to terrain-following coordinate models. This is due to the typically higher resolution of the ice–ocean boundary layer region in terrain following models, which allows better representation of a thin meltwater layer, increased stratification, and as a result, better insulation of the ice from water below. We show that a terrain-following model, a z-level coordinate model and a hybrid approach give similar results when the effective vertical resolution adjacent to the ice shelf base is similar, despite each model employing different paradigms for distributing meltwater fluxes and sampling tracers for melting. We provide a benchmark for thermodynamic ice shelf–ocean interaction with different model vertical coordinates and vertical resolutions, and suggest a framework for any future ice shelf–ocean thermodynamic parameterisations

Vertical processes and resolution impact ice shelf basal melting: A multi-model study

Understanding ice shelf–ocean interaction is fundamental to projecting the Antarctic ice sheet response to a warming climate. Numerical ice shelf–ocean models are a powerful tool for simulating this interaction, yet are limited by inherent model weaknesses and scarce observations, leading to parameterisations that are unverified and unvalidated below ice shelves. We explore how different models simulate ice shelf–ocean interaction using the 2nd Ice Shelf–Ocean Model Intercomparison Project (ISOMIP+) framework. Vertical discretisation and resolution of the ocean model are shown to have a significant effect on ice shelf basal melt rate, through differences in the distribution of meltwater fluxes and the calculation of thermal driving. Z-coordinate models, which generally have coarser vertical resolution in ice shelf cavities, may simulate higher melt rates compared to terrain-following coordinate models. This is due to the typically higher resolution of the ice–ocean boundary layer region in terrain following models, which allows better representation of a thin meltwater layer, increased stratification, and as a result, better insulation of the ice from water below. We show that a terrain-following model, a z-level coordinate model and a hybrid approach give similar results when the effective vertical resolution adjacent to the ice shelf base is similar, despite each model employing different paradigms for distributing meltwater fluxes and sampling tracers for melting. We provide a benchmark for thermodynamic ice shelf–ocean interaction with different model vertical coordinates and vertical resolutions, and suggest a framework for any future ice shelf–ocean thermodynamic parameterisations. © 2020 The Author

CELLO: A fast algorithm for Covariance Estimation

We present CELLO (Covariance Estimation and Learning through Likelihood Optimization), an algorithm for predicting the covariances of measurements based on any available informative features. This algorithm is intended to improve the accuracy and reliability of on-line state estimation by providing a principled way to extend the conventional fixed-covariance Gaussian measurement model. We show that in experiments, CELLO learns to predict measurement covariances that agree with empirical covariances obtained by manually annotating sensor regimes. We also show that using the learned covariances during filtering provides substantial quantitative improvement to the overall state estimate. © 2013 IEEE.United States. National Aeronautics and Space AdministrationSiemens Corporate ResearchUnited States. Office of Naval Research. Multidisciplinary University Research InitiativeMicro Autonomous Consortium Systems and Technolog