Richard Kitney - Academia.edu (original) (raw)

Papers by Richard Kitney

IEEE Transactions on Nanobioscience, 2002

The purpose of this paper is to describe automated techniques for the visualization and mapping o... more The purpose of this paper is to describe automated techniques for the visualization and mapping of articular cartilage in magnetic resonance (MR) images of the osteoarthritic knee. The MR sequences and analysis software which will be described allow the assessment of cartilage damage using a range of standard scanners. With high field strength systems it would be possible, using these techniques, to assess micro-damage. The specific aim of the paper is to develop and validate software for automated segmentation and thickness mapping of articular cartilage from three-dimensional (3-D) gradient-echo MR images of the knee. The method can also be used for MR-based assessment of tissue engineered grafts. Typical values of cartilage thickness over seven defined regions can be obtained in patients with osteoarthritis (OA) and control subjects without OA. Three groups of patients were studied. The first group comprised patients with moderate OA in the age range 45-73 years. The second group comprised asymptomatic volunteers of 50-65 years; the third group, younger volunteers selected by clinical interview, history and X-ray. In this paper, sagittal 3-D spoiled-gradient steady-state acquisition images were obtained using a 1.5-T GE whole-body scanner with a specialist knee coil. For validation bovine and porcine cadaveric knees were given artificial cartilage lesions and then imaged. The animal validations showed close agreement between direct lesion measurements and those obtained from the MR images. The feasibility of semi-automated segmentation is demonstrated. Regional cartilage thickness values are seen as having practical application for fully automated detection of OA lesions even down to the submicrometer level.

BMC Bioinformatics, 2012

Background: Hospitals nowadays have to serve numerous patients with limited medical staff and equ... more Background: Hospitals nowadays have to serve numerous patients with limited medical staff and equipment while maintaining healthcare quality. Clinical pathway informatics is regarded as an efficient way to solve a series of hospital challenges. To date, conventional research lacks a mathematical model to describe clinical pathways. Existing vague descriptions cannot fully capture the complexities accurately in clinical pathways and hinders the effective management and further optimization of clinical pathways.

BMC Systems Biology, 2007

His research interests are centered around ageing. This includes the study of the molecular pathw... more His research interests are centered around ageing. This includes the study of the molecular pathways that extend lifespan. His research uses both computational and wetlab techniques for modelling gene regulatory networks and predicting transcription factor binding sites.

International Congress Series, 2001

Proceedings of Computers in Cardiology Conference, 1993

Integrative Biology, 2011

A proliferation of new computational methods and software tools for synthetic biology design has ... more A proliferation of new computational methods and software tools for synthetic biology design has emerged in recent years but the field has not yet reached the stage where the design and construction of novel synthetic biology systems has become routine. To a large degree this is due to the inherent complexity of biological systems. However, advances in biotechnology and our scientific understanding have already enabled a number of significant achievements in this area. A key concept in engineering is the ability to assemble simpler standardised modules into systems of increasing complexity but it has yet to be adequately addressed how this approach can be applied to biological systems. In particular, the use of computer aided design tools is common in other engineering disciplines and it should eventually become centrally important to the field of synthetic biology if the challenge of dealing with the stochasticity and complexity of biological systems can be overcome.

Journal of The Royal Society Interface, 2009

We introduce microfluidics technologies as a key foundational technology for synthetic biology ex... more We introduce microfluidics technologies as a key foundational technology for synthetic biology experimentation. Recent advances in the field of microfluidics are reviewed and the potential of such a technological platform to support the rapid development of synthetic biology solutions is discussed.

PloS one, 2015

Biopolymers, such as poly-3-hydroxybutyrate (P(3HB)) are produced as a carbon store in an array o... more Biopolymers, such as poly-3-hydroxybutyrate (P(3HB)) are produced as a carbon store in an array of organisms and exhibit characteristics which are similar to oil-derived plastics, yet have the added advantages of biodegradability and biocompatibility. Despite these advantages, P(3HB) production is currently more expensive than the production of oil-derived plastics, and therefore, more efficient P(3HB) production processes would be desirable. In this study, we describe the model-guided design and experimental validation of several engineered P(3HB) producing operons. In particular, we describe the characterization of a hybrid phaCAB operon that consists of a dual promoter (native and J23104) and RBS (native and B0034) design. P(3HB) production at 24 h was around six-fold higher in hybrid phaCAB engineered Escherichia coli in comparison to E. coli engineered with the native phaCAB operon from Ralstonia eutropha H16. Additionally, we describe the utilization of non-recyclable waste as...

IET Synthetic Biology, 2007

The paper addresses the problem of designing and building a stable molecular based oscillator whi... more The paper addresses the problem of designing and building a stable molecular based oscillator which can be controlled in terms of both amplitude and frequency. A study of previous oscillators of this type showed that they are inherently unstable. To overcome this problem a design was chosen which is based on Lotka -Voltera dynamics. An important aspect of the work was the use of what we term the Engineering Cycle; that is, the cycle of system specification, design, modelling, implementation, and testing and validation. The Lotka -Voltera dynamic, in the context of a predation oscillator, amounts to a predator -prey approach. This is the basis of the oscillator design. The oscillator was designed and detailed modelling undertaken to establish the modes of the dynamic; how it could be tuned for stability; and how to control its amplitude and frequency. The biological implementation of the design was undertaken using a number of BioBricks from the MIT registry (http://parts.mit.edu/registry/index.php/Main_Page), together with a number of parts which we designed and built.

BMC Systems Biology, 2007

IEEE Transactions on Nanobioscience, 2002

The purpose of this paper is to describe automated techniques for the visualization and mapping o... more The purpose of this paper is to describe automated techniques for the visualization and mapping of articular cartilage in magnetic resonance (MR) images of the osteoarthritic knee. The MR sequences and analysis software which will be described allow the assessment of cartilage damage using a range of standard scanners. With high field strength systems it would be possible, using these techniques, to assess micro-damage. The specific aim of the paper is to develop and validate software for automated segmentation and thickness mapping of articular cartilage from three-dimensional (3-D) gradient-echo MR images of the knee. The method can also be used for MR-based assessment of tissue engineered grafts. Typical values of cartilage thickness over seven defined regions can be obtained in patients with osteoarthritis (OA) and control subjects without OA. Three groups of patients were studied. The first group comprised patients with moderate OA in the age range 45-73 years. The second group comprised asymptomatic volunteers of 50-65 years; the third group, younger volunteers selected by clinical interview, history and X-ray. In this paper, sagittal 3-D spoiled-gradient steady-state acquisition images were obtained using a 1.5-T GE whole-body scanner with a specialist knee coil. For validation bovine and porcine cadaveric knees were given artificial cartilage lesions and then imaged. The animal validations showed close agreement between direct lesion measurements and those obtained from the MR images. The feasibility of semi-automated segmentation is demonstrated. Regional cartilage thickness values are seen as having practical application for fully automated detection of OA lesions even down to the submicrometer level.

BMC Bioinformatics, 2012

Background: Hospitals nowadays have to serve numerous patients with limited medical staff and equ... more Background: Hospitals nowadays have to serve numerous patients with limited medical staff and equipment while maintaining healthcare quality. Clinical pathway informatics is regarded as an efficient way to solve a series of hospital challenges. To date, conventional research lacks a mathematical model to describe clinical pathways. Existing vague descriptions cannot fully capture the complexities accurately in clinical pathways and hinders the effective management and further optimization of clinical pathways.

BMC Systems Biology, 2007

His research interests are centered around ageing. This includes the study of the molecular pathw... more His research interests are centered around ageing. This includes the study of the molecular pathways that extend lifespan. His research uses both computational and wetlab techniques for modelling gene regulatory networks and predicting transcription factor binding sites.

International Congress Series, 2001

Proceedings of Computers in Cardiology Conference, 1993

Integrative Biology, 2011

A proliferation of new computational methods and software tools for synthetic biology design has ... more A proliferation of new computational methods and software tools for synthetic biology design has emerged in recent years but the field has not yet reached the stage where the design and construction of novel synthetic biology systems has become routine. To a large degree this is due to the inherent complexity of biological systems. However, advances in biotechnology and our scientific understanding have already enabled a number of significant achievements in this area. A key concept in engineering is the ability to assemble simpler standardised modules into systems of increasing complexity but it has yet to be adequately addressed how this approach can be applied to biological systems. In particular, the use of computer aided design tools is common in other engineering disciplines and it should eventually become centrally important to the field of synthetic biology if the challenge of dealing with the stochasticity and complexity of biological systems can be overcome.

Journal of The Royal Society Interface, 2009

We introduce microfluidics technologies as a key foundational technology for synthetic biology ex... more We introduce microfluidics technologies as a key foundational technology for synthetic biology experimentation. Recent advances in the field of microfluidics are reviewed and the potential of such a technological platform to support the rapid development of synthetic biology solutions is discussed.

PloS one, 2015

Biopolymers, such as poly-3-hydroxybutyrate (P(3HB)) are produced as a carbon store in an array o... more Biopolymers, such as poly-3-hydroxybutyrate (P(3HB)) are produced as a carbon store in an array of organisms and exhibit characteristics which are similar to oil-derived plastics, yet have the added advantages of biodegradability and biocompatibility. Despite these advantages, P(3HB) production is currently more expensive than the production of oil-derived plastics, and therefore, more efficient P(3HB) production processes would be desirable. In this study, we describe the model-guided design and experimental validation of several engineered P(3HB) producing operons. In particular, we describe the characterization of a hybrid phaCAB operon that consists of a dual promoter (native and J23104) and RBS (native and B0034) design. P(3HB) production at 24 h was around six-fold higher in hybrid phaCAB engineered Escherichia coli in comparison to E. coli engineered with the native phaCAB operon from Ralstonia eutropha H16. Additionally, we describe the utilization of non-recyclable waste as...

IET Synthetic Biology, 2007

The paper addresses the problem of designing and building a stable molecular based oscillator whi... more The paper addresses the problem of designing and building a stable molecular based oscillator which can be controlled in terms of both amplitude and frequency. A study of previous oscillators of this type showed that they are inherently unstable. To overcome this problem a design was chosen which is based on Lotka -Voltera dynamics. An important aspect of the work was the use of what we term the Engineering Cycle; that is, the cycle of system specification, design, modelling, implementation, and testing and validation. The Lotka -Voltera dynamic, in the context of a predation oscillator, amounts to a predator -prey approach. This is the basis of the oscillator design. The oscillator was designed and detailed modelling undertaken to establish the modes of the dynamic; how it could be tuned for stability; and how to control its amplitude and frequency. The biological implementation of the design was undertaken using a number of BioBricks from the MIT registry (http://parts.mit.edu/registry/index.php/Main_Page), together with a number of parts which we designed and built.

BMC Systems Biology, 2007