Knowledge representation for data integration and exploration in translational medicine

Tese de doutoramento, Informática (Bioinformática), Universidade de Lisboa, Faculdade de Ciências, 2014

Exercise Prescription for Patients with Non-specific Chronic Low Back Pain: a Qualitative Exploration of Decision Making in Physiotherapy Practice

Background: Providing an effective exercise prescription process for patients with non-specific chronic low back pain (NSCLBP) is a challenging task. Emerging research has indicated that partnership in care and shared decision making are important for people with NSCLBP and calls for further investigation into the approaches used to prescribe exercise. Objective: To explore how shared decision making and patient partnership are addressed by physiotherapists in the process of exercise prescription for patients with NSCLBP. Design: A qualitative study using a philosophical hermeneutic approach. Methods: Eight physiotherapists were each observed on three occasions undertaking their usual clinical activities (total n=24 observations). They conducted brief interviews after each observation and a later in depth semi-structured interview. Iterative hermeneutic strategies were used to interpret the texts and identify the characteristics and processes of exercise prescription for patients with NSCLBP. Findings: The findings revealed how physiotherapy practice often resulted in unequal possibilities for patient participation which were in turn linked to the physiotherapists? assumptions about the patients, clinical orientation, cognitive and decision making processes. Three linked themes emerged: (1) I want them to exercise, (2) Which exercise? - the tension between evidence and everyday practice and (3) Compliance-orientated more than concordance based. Conclusions: This research, by focusing on a patient-centred approach, makes an important contribution to the body of evidence relating to the management of NSCLBP. It challenges physiotherapists to critically appraise their approaches to the prescription of exercise therapy in order to improve outcomes for these patients.

Expert Insight into the Assessment of Competence in Cognitive–behavioural Therapy: a Qualitative Exploration of Experts' Experiences, Opinions and Recommendations

To offer insight into how cognitive–behavioural therapy (CBT) competence is defined, measured and evaluated and to highlight ways in which the assessment of CBT competence could be further improved, the current study utilizes a qualitative methodology to examine CBT experts’ (N = 19) experiences of conceptualizing and assessing the competence of CBT therapists. Semi-structured interviews were used to explore participants’ experiences of assessing the competence of CBT therapists. Interview transcripts were then analysed using interpretative phenomenological analysis in order to identify commonalities and differences in the way CBT competence is evaluated. Four superordinate themes were identified: (i) what to assess, the complex and fuzzy concept of CBT competence; (ii) how to assess CBT competence, selecting from the toolbox of assessment methods; (iii) who is best placed to assess CBT competence, expertise and independence; and (iv) pitfalls, identifying and overcoming assessment biases. Priorities for future research and ways in which the assessment of CBT competence could be further improved are discussed in light of these findings.

The Impact of Thought Speed and Variability on Psychological State and Threat Perception: Further Exploration of the Theory of Mental Motion

Thought speed and variability are purportedly common features of specific psychological states, such as mania and anxiety. The present study explored the independent and combinational influence of these variables upon condition-specific symptoms and affective state, as proposed by Pronin and Jacobs’ (Perspect Psychol Sci, 3:461–485, 2008) theory of mental motion. A general population sample was recruited online (N = 263). Participants completed a thought speed and variability manipulation task, inducing a combination of fast/slow and varied/repetitive thought. Change in mania and anxiety symptoms was assessed through direct self-reported symptom levels and indirect, processing bias assessment (threat interpretation). Results indicated that fast and varied thought independently increased self-reported mania symptoms. Affect was significantly less positive and more negative during slow thought. No change in anxiety symptoms or threat interpretation was found between manipulation conditions. No evidence for the proposed combinational influence of speed and variability was found. Implications and avenues for therapeutic intervention are discussed.

Towards the End of Life: an In-depth Exploration of the Role of Admiral Nursing in Dementia Care (Innovative Practice)

There are approximately 150 Admiral Nurses in the UK who work alongside other health and social care professionals to support people with dementia and their family carers. However, the stigma of the disease and the lack of recognition that dementia is a life limiting illness have led to neglect in addressing the end of life challenges. The small in-depth study reported here aimed to add to an extremely limited formal evidence base for the effectiveness of this approach and to develop a greater understanding of the range of knowledge and skills required of them in ensuring they are better able to support families in the later stages of the illness. Findings focus on the experiences of family carers, the impact of performing the Admiral Nurse role and the use of qualitative measures in this setting.

An Exploration of the Use of Coaching and Mentoring in the Supervision of Doctoral Students in UK University Business Schools

Purpose: to consider and evaluate the student and supervisor experience of doctoral supervision (dyadic and triadic) and specifically the value of using coaching and mentoring approaches (process and relationship) in supervisory practice. Design/methodology/approach: phase one is a mixed methods study exploring the use of coaching and mentoring in doctoral supervision on traditional and taught doctoral programmes in one UK university business school. The focus is on developing a conceptual model for doctoral supervisory practice for the transfer of learning and the improvement of practice. Phase two will be a collaborative action research study in a range of UK university business schools to use, reflect on and refine the conceptual model of supervision. Findings: the initial findings from phase one will be reported on at the conference presentation. Research limitations/implications: we have tentative agreements from four UK university business schools for phase two (subject to ethics approval). Practical implications: students and supervisors participating in the research will benefit from having the opportunity to review and improve their practice; the participating business schools will have the opportunity to review and potentially revise their doctoral student and supervisor training; and a business school’s reputation for high quality doctoral supervision could be enhanced. Social implications: could potentially benefit numerous future students and supervisors across a wide range of UK university business schools. Originality/value: there does not appear to be any previously published research on the use of coaching and mentoring in doctoral supervision in UK university business schools for the transfer of learning and improvement of practice.

An exploration of pre-attentive visual discrimination using event-related potentials

The Mismatch Negativity (MMN) has been characterised as a ‘pre-attentive’ component of an Event-Related Potential (ERP) that is related to discriminatory processes. Although well established in the auditory domain, characteristics of the MMN are less well characterised in the visual domain. The five main studies presented in this thesis examine visual cortical processing using event-related potentials. Novel methodologies have been used to elicit visual detection and discrimination components in the absence of a behavioural task. Developing paradigms in which a behavioural task is not required may have important clinical applications for populations, such as young children, who cannot comply with the demands of an active task. The ‘pre-attentive’ nature of visual MMN has been investigated by modulating attention. Generators and hemispheric lateralisation of visual MMN have been investigated by using pertinent clinical groups. A three stimulus visual oddball paradigm was used to explore the elicitation of visual discrimination components to a change in the orientation of stimuli in the absence of a behavioural task. Monochrome stimuli based on pacman figures were employed that differed from each other only in terms of the orientation of their elements. One such stimulus formed an illusory figure in order to capture the participant’s attention, either in place of, or alongside, a behavioural task. The elicitation of a P3a to the illusory figure but not to the standard or deviant stimuli provided evidence that the illusory figure captured attention. A visual MMN response was recorded in a paradigm with no task demands. When a behavioural task was incorporated into the paradigm, a P3b component was elicited consistent with the allocation of attentional resources to the task. However, visual discrimination components were attenuated revealing that the illusory figure was unable to command all attentional resources from the standard deviant transition. The results are the first to suggest that the visual MMN is modulated by attention. Using the same three stimulus oddball paradigm, generators of visual MMN were investigated by recording potentials directly from the cortex of an adolescent undergoing pre-surgical evaluation for resection of a right anterior parietal lesion. To date no other study has explicitly recorded activity related to the visual MMN intracranially using an oddball paradigm in the absence of a behavioural task. Results indicated that visual N1 and visual MMN could be temporally and spatially separated, with visual MMN being recorded more anteriorly than N1. The characteristic abnormality in retinal projections in albinism afforded the opportunity to investigate each hemisphere in relative isolation and was used, for the first time, as a model to investigate lateralisation of visual MMN and illusory contour processing. Using the three stimulus oddball paradigm, no visual MMN was elicited in this group, and so no conclusions regarding the lateralisation of visual MMN could be made. Results suggested that both hemispheres were equally capable of processing an illusory figure. As a method of presenting visual test stimuli without conscious perception, a continuous visual stream paradigm was developed that used a briefly presented checkerboard stimulus combined with masking for exploring stimulus detection below and above subjective levels of perception. A correlate of very early cortical processing at a latency of 60-80 ms (CI) was elicited whether stimuli were reported as seen or unseen. Differences in visual processing were only evident at a latency of 90 ms (CII) implying that this component may represent a correlate of visual consciousness/awareness. Finally, an oddball sequence was introduced into the visual stream masking paradigm to investigate whether visual MMN responses could be recorded without conscious perception. The stimuli comprised of black and white checkerboard elements differing only in terms of their orientation to form an x or a +. Visual MMN was not recorded when participants were unable to report seeing the stimulus. Results therefore suggest that behavioural identification of the stimuli was required for the elicitation of visual MMN and that visual MMN may require some attentional resources. On the basis of these studies it is concluded that visual MMN is not entirely independent of attention. Further, the combination of clinical and non-clinical investigations provides a unique opportunity to study the characterisation and localisation of putative mechanisms related to conscious and non-conscious visual processing.

“I’m Not Waving, I’m Drowning”: An Autoethnographical Exploration of Biographical Disruption and Reconstruction During Recovery From Prescribed Benzodiazepine Use

Benzodiazepines are group of drugs used mainly as sedatives, hypnotics, muscle relaxants, and anti-epileptics. Tapering off benzodiazepines is, for some users, a painful, traumatic, and protracted process. In this article, I use an autoethnographic approach, adopting the metaphor of water, to examine heuristically my experience of iatrogenic illness and recovery. I draw on personal journals and blog entries and former users’ narratives to consider the particular form of biographical disruption associated with benzodiazepines and the processes involved in identity reconstruction. I emphasize the role of the online community in providing benzodiazepine users such as myself with a co-cultural community through which to share a voice and make sense of our experiences. I explain how the success stories of former users provided me with the hope that I, the “medical victim,” could become the “victor” and in the process construct a new life and fresh identity.

Proposta metodológica para avaliação preliminar de jazigos de shale gas

O potencial de um reservatório de shale gas e influenciado por um grande número de fatores, tais como a sua mineralogia e textura, o seu tipo e maturação de querogénio, a saturação de fluidos, os mecanismos de armazenamento de gás, a profundidade do reservatório e a temperatura e pressão de poros. Nesse sentido, o principal objetivo desta tese foi estabelecer uma metodologia de avaliação preliminar de potenciais jazigos de shale gas (estudo de afloramentos com base numa litoestratigrafia de alta resolução), que foi posteriormente aplicada na Formação de Vale das Fontes (Bacia Lusitânica, Portugal). Esta tese tem a particularidade de contribuir, não só para o aprofundamento da informação a nível geoquímico do local, mas também na abordagem inovadora que permitiu a caracterização petrofísica da Formação de Vale das Fontes. Para a aplicação da metodologia estabelecida, foi necessária a realização dos seguintes ensaios laboratoriais: Rock-Eval 6, picnometria de gás hélio, ensaio de resistência a compressão simples, Darcypress e a difracção de raios-X, aplicando o método de Rietveld. Os resultados obtidos na análise petrofísica mostram uma formação rochosa de baixa porosidade que segundo a classificação ISRM, e classificada como ”Resistente”, para alem de revelar comportamento dúctil e elevado índice de fragilidade. A permeabilidade média obtida situa a Formação no intervalo correspondente as permeabilidades atribuídas aos jazigos de tigh gas, indicando a necessidade de fracturação hidráulica, no caso de uma eventual exploração de hidrocarbonetos, enquanto a difracção de raios-X destaca a calcite, o quartzo e os filossilicatos como os minerais mais presentes na Formação. Do ponto de vista geoquímico, os resultados obtidos mostram que apesar do considerável teor médio de carbono orgânico total, a natureza da matéria orgânica analisada e maioritariamente imatura, composta, principalmente, por querogénio do tipo IV, o que indica a incapacidade de a formação gerar hidrocarbonetos em quantidades economicamente exploráveis.

TIGRE - An autonomous ground robot for outdoor exploration

13th International Conference on Autonomous Robot Systems (Robotica), 2013

On and off air: an ethnographic exploration of minority radio in Portugal

Taking a Media Anthropology’s approach to dynamics of mediated selfrepresentation in migratory contexts, this thesis starts by mapping radio initiatives produced by, for and/or with migrants in Portugal. To further explore dynamics of support of initial settlement in the country, community-making, cultural reproduction, and transnational connectivity - found both in the mapping stage and the minority media literature (e.g. Kosnick, 2007; Rigoni & Saitta, 2012; Silverstone & Georgiou, 2005) - a case study was selected: the station awarded with the first bilingual license in Portugal. The station in question caters largely to the British population presenting themselves as “expats” and residing in the Algarve. The ethnographic strategy to research it consisted of “following the radio” (Marcus, 1995) beyond the station and into the events and establishments it announces on air, so as to relate production and consumption realms. The leading research question asks how does locally produced radio play into “expats” processes of management of cultural identity – and what are the specificities of its role? Drawing on conceptualizations of lifestyle migration (Benson & O’Reilly, 2009), production of locality (Appadurai 1996) and the public sphere (Butsch, 2007; Calhoun & et al, 1992; Dahlgren, 2006), this thesis contributes to valuing radio as a productive gateway to research migrants’ construction of belonging, to inscribe a counterpoint in the field of minority media, and to debate conceptualizations of migratory categories and flows. Specifically, this thesis argues that the station fulfills similar roles to other minority radio initiatives but in ways that are specific to the population being catered to. Namely, unlike other minority stations, radio facilitates the process of transitioning between categories along on a continuum linking tourists and migrants. It also reflects and participates in strategies of reterritorialization that rest on functional and partial modes of incorporation. While contributing to sustain a translocality (Appadurai, 1996) it indexes and fosters a stance of connection that is symbolically and materially connected to the UK and other “neighborhoods” but is, simultaneously, oriented to engaging with the Algarve as “home”. Yet, besides reifying a British cultural identity, radio’s oral, repetitive and ephemeral discourse particularly trivializes the reproduction of an ambivalent stance of connection with place that is shared by other “expats”. This dynamic is related to migratory projects driven by social imaginaries fostered by international media that stimulate the search for idealized ways of living, which the radio associates with the Algarve. While recurrently localizing and validating the narrative projecting an idealized “good life”, radio amplifies dynamics among migrants that seem to reaffirm the migratory move as a good choice.

Valuing an offshore exploration project through real options analysis

This thesis applied real options analysis to the valuation of an offshore oil exploration project, taking into consideration the several options typically faced by the management team of these projects. The real options process is developed under technical and price uncertainties, where it is considered that the mean reversion stochastic process is more adequate to describe the movement of oil price throught time. The valuation is realized to two case scenarios, being the first a simplified approach to develop the intuition of the used concepts, and the later a more complete cases that is resolved using both the binomial and trinomial processes to describe oil price movement. Real options methodology demonstrated to be capable of assessing and valuing the projects options, and of overcoming common capital budgeting methodologies flexibility limitation. The added value of the application of real options is evident, but so is the method's increased complexity, which adversely influence its widespread implementation.

Exploration of the visual system : Part 2. In vivo analysis methods : virtual-reality optomotor system, fundus examination and fluorescent angiography

The mouse has emerged as an animal model for many diseases. At IRO, we have used this animal to understand the development of many eye diseases and treatment of some of them. Precise evaluation of vision is a prerequisite for both these approaches. In this unit we describe three ways to measure vision: testing the optokinetic response, and evaluating the fundus by direct observation and by fluorescent angiography.