Ryan Imms

A high performance biometric signal and image processing method to reveal blood perfusion towards 3D oxygen saturation mapping

Non-contact imaging photoplethysmography (PPG) is a recent development in the field of physiological data acquisition, currently undergoing a large amount of research to characterize and define the range of its capabilities. Contact-based PPG techniques have been broadly used in clinical scenarios for a number of years to obtain direct information about the degree of oxygen saturation for patients. With the advent of imaging techniques, there is strong potential to enable access to additional information such as multi-dimensional blood perfusion and saturation mapping. The further development of effective opto-physiological monitoring techniques is dependent upon novel modelling techniques coupled with improved sensor design and effective signal processing methodologies. The biometric signal and imaging processing platform (bSIPP) provides a comprehensive set of features for extraction and analysis of recorded iPPG data, enabling direct comparison with other biomedical diagnostic tools such as ECG and EEG. Additionally, utilizing information about the nature of tissue structure has enabled the generation of an engineering model describing the behaviour of light during its travel through the biological tissue. This enables the estimation of the relative oxygen saturation and blood perfusion in different layers of the tissue to be calculated, which has the potential to be a useful diagnostic tool.

Multiscale systems modeling of the tetralogy of Fallot

This paper provides a first description of a multiscale systems modeling approach applied to the congenital birth defect known as the tetralogy of Fallot. The multiscale approach adopted owes a lot to the effort of the world-wide physiome consortium and the work of research groups within the European Union on the Virtual Physiological Human. Both a spatial scale and time scale are used to establish the systems boundaries of the application. The tetralogy of Fallot includes up to four simultaneously occurring anatomic abnormalities that underpin the defect. The use of finite state machines and cellular automata pave the way to understand the processes in time and space that contribute to the defect.

Multiscale information modelling for heart morphogenesis

Science is made feasible by the adoption of common systems of units. As research has become more data intensive, especially in the biomedical domain, it requires the adoption of a common system of information models, to make explicit the relationship between one set of data and another, regardless of format. This is being realised through the OBO Foundry to develop a suite of reference ontologies, and NCBO Bioportal to provide services to integrate biomedical resources and functionality to visualise and create mappings between ontology terms. Biomedical experts tend to be focused at one level of spatial scale, be it biochemistry, cell biology, or anatomy. Likewise, the ontologies they use tend to be focused at a particular level of scale. There is increasing interest in a multiscale systems approach, which attempts to integrate between different levels of scale to gain understanding of emergent effects. This is a return to physiological medicine with a computational emphasis, exemplified by the worldwide Physiome initiative, and the European Union funded Network of Excellence in the Virtual Physiological Human. However, little work has been done on how information modelling itself may be tailored to a multiscale systems approach. We demonstrate how this can be done for the complex process of heart morphogenesis, which requires multiscale understanding in both time and spatial domains. Such an effort enables the integration of multiscale metrology.

Towards multiscale systems modeling of endocardial to mesenchymal transition

Cell behavior during endocardial to mesenchymal transition (EMT) was simulated using the cellular Potts formalism in Compucell 3D. The processes of loss of endocardial cohesion and invasion into the extracellular matrix (ECM) were stimulated by changing surface energy parameters. The simulations match in vitro results which suggest that endocardial motility on the surface of collagen gel can be induced separately from 3D invasion of the gel, via Notch signaling in the absence of BMP2. A principle by which the rate of mitosis would regulate the monolayer was demonstrated; suggesting a route for Vascular Endothelial Growth Factor (VEGF) control of EMT. A conceptual model of the system of protein interactions during EMT was assembled from multiple studies. A route for subcellular models to be formalized as Systems Biology Markup Language (SBML) differential equations is indicated. Scale linking would be achieved through Compucell 3D periodically integrating the SBML models for each cell during a simulation run, and updating parameters for protein concentrations assigned to individual cells. The surface energy parameters for the cells would be recalculated at each step from their simulated protein concentrations. Such scale linking opens up the potential for complexity to be gradually introduced, while maintaining experimental validation.

Engineering Biology: Model Conceptualisation and Realisation:

A model of the lysis-lysogeny decision cycle of the Phage-λ virus has been re-implemented using standard engineering tools. The model is based on previous systems biology-based work and is constructed using the biological knowledge of the protein signalling networks within the virus. It explores how the emergent effects from the protein interactions produce the observed lysis-lysogeny behaviour. The software tools used (LabVIEWTM and MATLABTM) were chosen as they do not require specialised biochemical knowledge and have a wide industrial user base. This modelling is done as part of Project Fallot at Loughborough University, which is producing multiscale models of congenital heart disease. Part of this research requires a model of Delta-Notch protein signalling. Comment is made on the applications of the implemented modelling technique for modelling of Delta Notch protein signalling in cells.

Electrically conductive adhesive enable to manufacture high performance patch probe for non-invasive physiological assessment

A reflection-mode photoplethysmographic (rPPG) patch probe has been researched to improve its performance for non-invasive physiological assessment through electrically conductive adhesives (ECAs) based manufacture processes. Special PiN photodiodes and Light Emitting Diodes (LEDs) were mounted on a flexible printed circuit to reach the objectives of both sensitivity and stability, and user comfort as well. The trial rPPG probes were successfully manufactured and evaluated in the house. The results gained from this study shown the functions of the probe could be fully realized by ECAs. The preliminary outcome demonstrates the suitability for the cardiovascular assessment.

3D Simulation of an invitro Epithelial to Mesenchymal Transition

A 3D simulation of in vitro epithelial to mesenchymal transition (EMT) is presented. The simulation uses Compucell3D to realize a cellular Potts model of this process. The purpose of the model is to test the hypothesis that EMT can be achieved through a combination of a) the loss of endocardial cohesion; and b) a gain of endocardial to extracellular matrix adhesion. The results of the simulation demonstrate confirmation of the hypothesis. A mechanism by which EMT could be regulated by mitosis is demonstrated. Further, the implication of the study to heart development is explored.