Action design research: a comparison with canonical action research and design science

This research in progress paper addresses the IS issue in relation to conducting relevant research while keeping academic rigor. In particular, it contributes to the ongoing academic conversation around the investigation on how to incor-porate action in design science research. In this document the philosophical underpinnings of the recently proposed methodology called Action Design Re-search [1] are derived, outlined and integrated into Burrel and Morgan’s Par-adigmatic Framework (1979)[6]. The results so far show how Action Design Research can be considered as a particular case of Design Science Research (rather than a methodology closely related to Action Research) although they can assume two different epistemological positions. From these philosophical perspectives, future works will involve the inclusion of actual research projects using the three different methodologies. The final goal is to outline and structure the divergences and similarities of Action Design Research with Design Science Research and Canonical Action Research.

Genome-scale analyses of health-promoting bacteria: probiogenomics

The human body is colonized by an enormous population of bacteria (microbiota) that provides the host with coding capacity and metabolic activities. Among the human gut microbiota are health-promoting indigenous species (probiotic bacteria) that are commonly consumed as live dietary supplements. Recent genomics-based studies (probiogenomics) are starting to provide insights into how probiotic bacteria sense and adapt to the gastrointestinal tract environment. In this Review, we discuss the application of probiogenomics in the elucidation of the molecular basis of probiosis using the well-recognized model probiotic bacteria genera Bifidobacterium and Lactobacillus as examples.

THAWS: automated wireless sensor network development and deployment

This research focuses on the design and implementation of a tool to speed-up the development and deployment of heterogeneous wireless sensor networks. The THAWS (Tyndall Heterogeneous Automated Wireless Sensors) tool can be used to quickly create and configure application-specific sensor networks. THAWS presents the user with a choice of options, in order to characterise the desired functionality of the network. With this information, THAWS generates the necessary code from pre-written templates and well-tested, optimized software modules. This is then automatically compiled to form binary files for each node in the network. Wireless programming of the network completes the task of targeting the wireless network towards a specific sensing application. THAWS is an adaptable tool that works with both homogeneous and heterogeneous networks built from wireless sensor nodes that have been developed in the Tyndall National Institute.

Addressing non-linear hardware limitations and extending network coverage area for power aware wireless sensor networks

Science Foundation Ireland (07/CE/11147); Irish Research Council for Science Engineering and Technology (Embark Initiative)

Zinc finger nuclease gene repair as a treatment for cystinosis

Cystinosis is a multi-system autosomal recessive disorder caused by mutations and/or deletions in both alleles of CTNS, a gene encoding for the low pH dependent lysosomal cystine exporter cystinosin. Cystinosis occurs in approximately 1:200,000 newborns worldwide and is characterised by an accumulation of cystine in the lysosomes. The most severe form of the disorder is nephropathic cystinosis presenting Fanconi syndrome and leads without treatment to an end-stage renal failure before the age of ten. The only treatment available so far is cysteamine therapy, which delays disease progression by five years, but does not provide a cure for cystinosis patients. Current gene and cell based therapeutic approaches have not yet provided a suitable alternative. A potentially approach for a long-term treatment could be to generate autologous gene–modified stem cells by repairing the gene. Zinc Finger Nucleases (ZFNs) serve as a tool to increase HDR up to a 200,000-fold by introducing a double-stranded break (DSB). Thus, simple mutations in the CTNS gene could be corrected by introduction of a double-stranded break using ZFNs to boost the process of HDR with a suitable donor DNA sequence. A permanent repair of the most common lesion CTNS, a 57 kb deletion, could be achieved by ZFN-mediated HDR using a minigene CTNS promoter/cDNA construct. The thesis describes the design and testing of seven zinc finger nuclease pairs for their cleavage activity in vitro and in cellulo.. A highly sensitive assay to detect even low levels of ZFN-mediated HDR was also developed. Finally, to further investigate the role of autophagy in tissue injury in cystinotic cells an assay to monitor autophagy levels in the cells was successfully developed. This assay provides the opportunity to demonstrate functional restoration of CTNS after successful ZFN-HDR in cystinotic cells.

Digital signal processing and artificial intelligence for the automated classification of food allergy

As a by-product of the ‘information revolution’ which is currently unfolding, lifetimes of man (and indeed computer) hours are being allocated for the automated and intelligent interpretation of data. This is particularly true in medical and clinical settings, where research into machine-assisted diagnosis of physiological conditions gains momentum daily. Of the conditions which have been addressed, however, automated classification of allergy has not been investigated, even though the numbers of allergic persons are rising, and undiagnosed allergies are most likely to elicit fatal consequences. On the basis of the observations of allergists who conduct oral food challenges (OFCs), activity-based analyses of allergy tests were performed. Algorithms were investigated and validated by a pilot study which verified that accelerometer-based inquiry of human movements is particularly well-suited for objective appraisal of activity. However, when these analyses were applied to OFCs, accelerometer-based investigations were found to provide very poor separation between allergic and non-allergic persons, and it was concluded that the avenues explored in this thesis are inadequate for the classification of allergy. Heart rate variability (HRV) analysis is known to provide very significant diagnostic information for many conditions. Owing to this, electrocardiograms (ECGs) were recorded during OFCs for the purpose of assessing the effect that allergy induces on HRV features. It was found that with appropriate analysis, excellent separation between allergic and nonallergic subjects can be obtained. These results were, however, obtained with manual QRS annotations, and these are not a viable methodology for real-time diagnostic applications. Even so, this was the first work which has categorically correlated changes in HRV features to the onset of allergic events, and manual annotations yield undeniable affirmation of this. Fostered by the successful results which were obtained with manual classifications, automatic QRS detection algorithms were investigated to facilitate the fully automated classification of allergy. The results which were obtained by this process are very promising. Most importantly, the work that is presented in this thesis did not obtain any false positive classifications. This is a most desirable result for OFC classification, as it allows complete confidence to be attributed to classifications of allergy. Furthermore, these results could be particularly advantageous in clinical settings, as machine-based classification can detect the onset of allergy which can allow for early termination of OFCs. Consequently, machine-based monitoring of OFCs has in this work been shown to possess the capacity to significantly and safely advance the current state of clinical art of allergy diagnosis

Towards a cognitive neurobiology of brain-gut axis disorders

The past two decades have seen substantial gains in our understanding of the complex processes underlying disturbed brain-gut communication in disorders such as irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). Despite a growing understanding of the neurobiology of brain-gut axis dysfunction, there is a relative paucity of investigations into how the various factors involved in dysregulating the brain-gut axis, including stress, immune activation and pain, could impact on fundamental brain processes such as cognitive performance. To this end, we proposed a cognitive neurobiology of brain-gut axis dysfunction and took a novel approach to examine how disturbed brain-gut interactions may manifest as altered cognitive performance in IBS and IBD, both cross-sectionally and prospectively. We have demonstrated that, disorders of the brain-gut axis are characterised by stable deficits in specific cognitive domains. Specifically, patients with IBS exhibit a consistent hippocampal mediated visuospatial memory impairment. In addition we have found evidence to suggest a similar visuospatial impairment in IBD. However, our most consistent finding within this population was that patients with Crohn’s disease exhibit impaired selective attention/ response inhibition on the classic Stroop interference test. These cognitive deficits may serve to perpetuate and sustain brain-gut axis dysfunction. Furthermore, this research has shed light on some of the underlying neurobiological mechanisms that may be mediating cognitive dysfunction in IBS. Our findings may have significant implications for the individual who suffers from a brain-gut axis disorder and may also inform future treatment strategies. Taken together, these findings can be incorporated into existing neurobiological models of brain-gut axis dysfunction, to develop a more comprehensive model accounting for the cognitive-neurobiology of brain-gut axis disorders. This has furthered our understanding of disease pathophysiology and may ultimately aid in both the diagnosis and treatment of these highly prevalent, but poorly understood disorders.

Akt signal transduction dysfunction in the 3xTg-AD mouse model of Alzheimer's disease

Alzheimer’s disease (AD) is an incurable neurodegenerative disorder, accounting for over 60% of all cases of dementia. The primary risk factor for AD is age, however several genetic and environmental factors are also involved. The pathological characteristics of AD include extracellular deposition of the beta-amyloid peptide (Aβ) and intraneuronal accumulation of neurofibrillary tangles (NFTs) made of aggregated paired helical filaments (PHFs) of the hyperphosphorylated tau protein, along with synaptic loss and neuronal death. There are numerous biochemical mechanisms involved in AD pathogenesis, however the reigning hypothesis points to toxic oligomeric Aβ species as the primary causative factor in a cascade of events leading to neuronal stress and dyshomeostasis that initiate abnormal regulation of tau. The insulin and IGF-1 receptors (IR, IGF-1R) are the primary activators of PI3- K/Akt through which they regulate cell growth, development, glucose metabolism, and learning and memory. Work in our lab and others shows increased Akt activity and phosphorylation of its downstream targets in AD brain, along with insulin and insulin-like growth factor-1 signalling (IIS) dysfunction. This is supported by studies of AD models in vivo and in vitro. Our group and others hypothesise that Aβ activates Akt through IIS to initiate a negative feedback mechanism that desensitises neurons to insulin/IGF-1, and sustains activation of Akt. In this study the functions of endogenous Akt, IR, and the insulin receptor substrate (IRS-1) were examined in relationship to Aβ and tau pathology in the 3xTg-AD mouse model, which contains three mutant human transgenes associated with familial AD or dementia. The 3xTg-AD mouse develops Aβ and tau pathology in a spatiotemporal manner that best recapitulates the progression of AD in human brain. Western blotting and immunofluorescent microscopy techniques were utilised in vivo and in vitro, to examine the relationship between IIS, Akt, and AD pathology. I first characterised in detail AD pathology in 3xTg-AD mice, where an age-related accumulation of intraneuronal Aβ and tau was observed in the hippocampal formation, amygdala, and entorhinal cortex, and at late stages (18 months), extracellular amyloid plaques and NFTs, primarily in the subiculum and the CA1 layer of the hippocampal formation. Increased activity of Akt, detected with antibody to phosphoSer473-Akt, was increased in 3xTg-AD mice compared to age-matched non-transgenic mice (non-Tg), and in direct correlation to the accumulation of Aβ and tau in neuronal somatodendritic compartments. Akt phosphorylates tau at residue Ser214 within a highly specific consensus sequence for Akt phosphorylation, and phosphoSer214-tau strongly decreases microtubule (MT) stabilisation by preventing tau-MT binding. PhosphoSer214-tau increased concomitantly with this in the same age-related and region-specific fashion. Polarisation of tau phosphorylation was observed, where PHF-1 (tauSer396/404) and phosphoSer214-tau both appeared early in 3xTg-AD mice in distinct neuronal compartments: PHF-1 in axons, and phosphoSer214-tau in neuronal soma and dendrites. At 18 months, phosphoSer214-tau strongly colocalised with NFTs positive for the PHF- 1 and AT8 (tauSer202/Thr205) phosphoepitopes. IR was decreased with age in 3xTg-AD brain and in comparison to age-matched non-Tg, and this was specific for brain regions containing Aβ, tau, and hyperactive Akt. IRS-1 was similarly decreased, and both proteins showed altered subcellular distribution. Phosphorylation of IRS-1Ser312 is a strong indicator of IIS dysfunction and insulin resistance, and was increased in 3xTg-AD mice with age and in relation to pathology. Of particular note was our observation that abberant IIS and Akt signalling in 3xTg-AD brain related to Aβ and tau pathology on a gross anatomical level, and specifically localised to the brain regions and circuitry of the perforant path. Finally, I conducted a preliminary study of the effects of synthetic Aβ oligomers on embryonic rat hippocampus neuronal cultures to support these results and those in the literature. Taken together, these novel findings provide evidence for IIS and Akt signal transduction dysfunction as the missing link between Aβ and tau pathogenesis, and contribute to the overall understanding of the biochemical mechanisms of AD.

Design and evaluation of novel microencapsulation technologies to enhance delivery of Ciclosporin

Drug delivery systems influence the various processes of release, absorption, distribution and elimination of drug. Conventional delivery methods administer drug through the mouth, the skin, transmucosal areas, inhalation or injection. However, one of the current challenges is the lack of effective and targeted oral drug administration. Development of sophisticated strategies, such as micro- and nanotechnology that can integrate the design and synthesis of drug delivery systems in a one-step, scalable process is fundamental in advancing the limitations of conventional processing techniques. Thus, the objective of this thesis is to evaluate novel microencapsulation technologies in the production of size-specific and target-specific drug-loaded particles. The first part of this thesis describes the utility of PDMS and silicon microfluidic flow focusing devices (MFFDs) to produce PLGA-based microparticles. The formation of uniform droplets was dependent on the surface of PDMS remaining hydrophilic. However, the durability of PDMS was limited to no more than 1 hour before wetting of the microchannel walls with dichloromethane and subsequent swelling occurred. Critically, silicon MFFDs revealed very good solvent compatibility and was sufficiently robust to withstand elevated fluid flow rates. Silicon MFFDs facilitated experiments to run over days with continuous use and re-use of the device with a narrower microparticle size distribution, relative to conventional production techniques. The second part of this thesis demonstrates an alternative microencapsulation technology, SmPill® minispheres, to target CsA delivery to the colon. Characterisation of CsA release in vitro and in vivo was performed. By modulating the ethylcellulose:pectin coating thickness, release of CsA in-vivo was more effectively controlled compared to current commercial CsA formulations and demonstrated a linear in-vitro in-vivo relationship. Coated minispheres were shown to limit CsA release in the upper small intestine and enhance localised CsA delivery to the colon.

Synthesis and characterization of oxide materials

Nanostructured materials are central to the evolution of future electronics and biomedical applications amongst other applications. This thesis is focused on developing novel methods to prepare a number of nanostructured metal oxide particles and films by a number of different routes. Part of the aim was to see how techniques used in nanoparticle science could be applied to thin film methods to develop functional surfaces. Wet-chemical methods were employed to synthesize and modify the metal oxide nanostructures (CeO2 and SiO2) and their structural properties were characterized through advanced X-ray diffraction, electron microscopy, photoelectron spectroscopy and other techniques. Whilst particulates have uses in many applications, their attachment to surfaces is of importance and this is frequently challenging. We examined the use of block copolymer methods to form very well defined metal oxide particulate-like structures on the surface of a number of substrates. Chapter 2 describes a robust method to synthesize various sized silica nanoparticles. As-synthesized silica nanoparticles were further functionalized with IR-820 and FITC dyes. The ability to create size controlled nanoparticles with associated (optical) functionality may have significant importance in bio-medical imaging. Thesis further describes how non-organic modified fluorescent particles might be prepared using inorganic oxides. A study of the concentrations and distributions of europium dopants within the CeO2 nanoparticles was undertaken and investigated by different microscopic and spectroscopic techniques. The luminescent properties were enhanced by doping and detailed explanations are reported. Additionally, the morphological and structural evolution and optical properties were correlated as a function of concentrations of europium doping as well as with further annealing. Further work using positron annihilation spectroscopy allowed the study of vacancy type defects formed due to europium doping in CeO2 crystallites and this was supported by complimentary UV-Vis spectra and XRD work. During the last few years the interest in mesoporous silica materials has increased due to their typical characteristics such as potential ultra-low dielectric constant materials, large surface area and pore volume, well-ordered and uniform pores with adjustable pores between 2 and 50 nm. A simple, generic and cost-effective route was used to demonstrate the synthesis of 2D mesoporous silica thin films over wafer scale dimensions in chapter 5. Lithographic resist and in situ hard mask block copolymer followed by ICP dry etching were used to fabricate mesoporous silica nanostructures. The width of mesoporous silica channels can be varied by using a variety of commercially available lithographic resists whereas depth of the mesoporous silica channels can be varied by altering the etch time. The crystal structure, morphology, pore arrangement, pore diameters, thickness of films and channels were determined by XRD, SEM, ellipsometry and the results reported. This project also extended work towards the study of the antimicrobial study of nanopatterned silver nanodot arrays formed using the block copolymer approach defined above. Silver nanodot arrays were successfully tested for antimicrobial activity over S. aureus and P. aeruginosa biofilms and results shows silver nanodots has good antimicrobial activity for both S. aureus and P. aeruginosa biofilms. Thus, these silver nanodot arrays shows a potential to be used as a substitute for the resolution of infection complications in many areas.

Supporting therapist engagement in evidence based practice: Developing a continuing education programme through participatory action research

Therapists find it challenging to integrate research evidence into their clinical decision-making because it may involve modifying their existing practices. Although continuing education (CE) programmes for evidence-based practice (EBP) have employed various approaches to increase individual practitioner’s knowledge and skills, these have been shown to have little impact in changing customary behaviours. To date, there has been little attempt to actively engage therapists as collaborators in developing educational processes concerning EBP. The researcher collaborated with seven clinical therapists (one occupational therapist, four physiotherapists and two speech and language therapists) enrolled in a new post-qualification Implementing Evidence in Therapy Practice (IETP) MSc module to monitor and adapt the learning programme over ten weeks. The participating therapists actively engaged in participatory action research (PAR) iterative cycles of reflecting→ planning→ acting→ observing→ reflecting with the researcher. Mixed methods were used to evaluate the IETP module and its influence on therapists’ subsequent engagement in EBP activities. Data were gathered immediately on completion of the module and five months later. Immediate post-module findings revealed four components as being important to the therapists: 1) characteristics of the learning environment; 2) acquisition of relevant EBP skills; 3) nature of the learning process; and 4) acquiring confidence. The two themes and sub-themes which emerged from individual interviews conducted five months post-module expanded on the four components already identified. Theme 1: Experiencing the learning (sub-themes: module organisation; learning is relational; improving the module); and theme 2: Enacting the learning through a new way of being (sub-themes: criticality and reflection; self agency; modelling EBP behaviours; positioning self in an EB work culture). The therapists’ perspectives had by then shifted from that of a learner to that of a clinician constructing a new sense of self as an evidence-based practitioner. Findings from this study underline the importance of the process of socially constructed knowledge and of empowering learners through collaboratively designed continuing education programmes. In the student-driven learning environment, therapists chose repetitive skill-building and authentic problem-solving activities which reflected the complexity of the environments to which they were expected to transfer their learning. These findings have implications for educators designing EBP continuing education programmes, during which students develop professional ways of being.

Developing a health and wellbeing platform in a living lab setting: An action design research study

The world’s population is rapidly aging, which affects healthcare budgets, resources, pensions and social security systems. Although most older adults prefer to live independently in their own home as long as possible, smart living solutions to support elderly people at home did not reach mass adoption, yet. To support people age-in-place a Living Lab is established in one of the metropolitan areas in the Netherlands. The main goal of the Living Lab is to develop an online health and wellbeing platform that matches service providers, caretakers and users and to implement that platform in one particular city district. In this paper we describe the narrative of the action design research process that will give researchers insight how to deal with complex multi-stakeholder design projects as well as cooperation issues to develop an artifact in a real-life setting.