888 resultados para FUNCTIONAL DATA ANALYSIS


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The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data publication contains measurements from the Continuous Surface Sampling System [CSSS] made during one campaign of the Tara Oceans Expedition. Water was pumped at the front of the vessel from ~2m depth, then de-bubbled and circulated to a Sea-Bird TSG temperature and conductivity sensor. System maintenance (instrument cleaning, flushing) was done approximately once a week and in port between successive legs. All data were stamped with a GPS.

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The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data publication contains measurements from the Continuous Surface Sampling System [CSSS] made during one campaign of the Tara Oceans Expedition. Water was pumped at the front of the vessel from ~2m depth, then de-bubbled and circulated to a Sea-Bird TSG temperature and conductivity sensor. System maintenance (instrument cleaning, flushing) was done approximately once a week and in port between successive legs. All data were stamped with a GPS.

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This research aims at studying the use of greeting cards, here understood as a literacy practice widely used in American society of the United States. In American culture, these cards become sources of information and memory about people‟s cycles of life, their experiences and their bonds of sociability enabled by means of the senses that the image and the word comprise. The main purpose of this work is to describe how this literacy practice occurs in American society. Theoretically, this research is based on studies of literacy (BARTON, HAMILTON, 1998; BAYHAM, 1995; HAMILTON, 2000; STREET, 1981, 1984, 1985, 1993, 2003), the contributions of social semiotics, associated with systemic-functional grammar (HALLIDAY; HASAN 1978, 1985, HALLIDAY, 1994, HALLIDAY; MATTHIESSEN, 2004), and the grammar of visual design (KRESS; LEITE-GARCIA, VAN LEEUWEN, 1997, 2004, 2006; KRESS; MATTHIESSEN, 2004). Methodologically, it is a study that falls within the qualitative paradigm of interpretative character, which adopts ethnographic tools in data generation. From this perspective, it makes use of “looking and asking” techniques (ERICKSON, 1986, p. 119), complemented by the technique of "registering", proposed by Paz (2008). The corpus comprises 104 printed cards, provided by users of this cultural artifact, from which we selected 24, and 11 e-cards, extracted from the internet, as well as verbalizations obtained by applying a questionnaire prepared with open questions asked in order to gather information about the perceptions and actions of these cards users with respect to this literacy practice. Data analysis reveals cultural, economic and social aspects of this practice and the belief that literacy practice of using printed greeting cards, despite the existence of virtual alternatives, is still very fruitful in American society. The study also allows users to comprehend that the cardholders position themselves and construct identities that are expressed in verbal and visual interaction in order to achieve the desired effect. As a result, it is understood that greeting cards are not unintentional, but loaded with ideology and power relations, among other aspects that are constitutive of them.

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Abstract

The goal of modern radiotherapy is to precisely deliver a prescribed radiation dose to delineated target volumes that contain a significant amount of tumor cells while sparing the surrounding healthy tissues/organs. Precise delineation of treatment and avoidance volumes is the key for the precision radiation therapy. In recent years, considerable clinical and research efforts have been devoted to integrate MRI into radiotherapy workflow motivated by the superior soft tissue contrast and functional imaging possibility. Dynamic contrast-enhanced MRI (DCE-MRI) is a noninvasive technique that measures properties of tissue microvasculature. Its sensitivity to radiation-induced vascular pharmacokinetic (PK) changes has been preliminary demonstrated. In spite of its great potential, two major challenges have limited DCE-MRI’s clinical application in radiotherapy assessment: the technical limitations of accurate DCE-MRI imaging implementation and the need of novel DCE-MRI data analysis methods for richer functional heterogeneity information.

This study aims at improving current DCE-MRI techniques and developing new DCE-MRI analysis methods for particular radiotherapy assessment. Thus, the study is naturally divided into two parts. The first part focuses on DCE-MRI temporal resolution as one of the key DCE-MRI technical factors, and some improvements regarding DCE-MRI temporal resolution are proposed; the second part explores the potential value of image heterogeneity analysis and multiple PK model combination for therapeutic response assessment, and several novel DCE-MRI data analysis methods are developed.

I. Improvement of DCE-MRI temporal resolution. First, the feasibility of improving DCE-MRI temporal resolution via image undersampling was studied. Specifically, a novel MR image iterative reconstruction algorithm was studied for DCE-MRI reconstruction. This algorithm was built on the recently developed compress sensing (CS) theory. By utilizing a limited k-space acquisition with shorter imaging time, images can be reconstructed in an iterative fashion under the regularization of a newly proposed total generalized variation (TGV) penalty term. In the retrospective study of brain radiosurgery patient DCE-MRI scans under IRB-approval, the clinically obtained image data was selected as reference data, and the simulated accelerated k-space acquisition was generated via undersampling the reference image full k-space with designed sampling grids. Two undersampling strategies were proposed: 1) a radial multi-ray grid with a special angular distribution was adopted to sample each slice of the full k-space; 2) a Cartesian random sampling grid series with spatiotemporal constraints from adjacent frames was adopted to sample the dynamic k-space series at a slice location. Two sets of PK parameters’ maps were generated from the undersampled data and from the fully-sampled data, respectively. Multiple quantitative measurements and statistical studies were performed to evaluate the accuracy of PK maps generated from the undersampled data in reference to the PK maps generated from the fully-sampled data. Results showed that at a simulated acceleration factor of four, PK maps could be faithfully calculated from the DCE images that were reconstructed using undersampled data, and no statistically significant differences were found between the regional PK mean values from undersampled and fully-sampled data sets. DCE-MRI acceleration using the investigated image reconstruction method has been suggested as feasible and promising.

Second, for high temporal resolution DCE-MRI, a new PK model fitting method was developed to solve PK parameters for better calculation accuracy and efficiency. This method is based on a derivative-based deformation of the commonly used Tofts PK model, which is presented as an integrative expression. This method also includes an advanced Kolmogorov-Zurbenko (KZ) filter to remove the potential noise effect in data and solve the PK parameter as a linear problem in matrix format. In the computer simulation study, PK parameters representing typical intracranial values were selected as references to simulated DCE-MRI data for different temporal resolution and different data noise level. Results showed that at both high temporal resolutions (<1s) and clinically feasible temporal resolution (~5s), this new method was able to calculate PK parameters more accurate than the current calculation methods at clinically relevant noise levels; at high temporal resolutions, the calculation efficiency of this new method was superior to current methods in an order of 102. In a retrospective of clinical brain DCE-MRI scans, the PK maps derived from the proposed method were comparable with the results from current methods. Based on these results, it can be concluded that this new method can be used for accurate and efficient PK model fitting for high temporal resolution DCE-MRI.

II. Development of DCE-MRI analysis methods for therapeutic response assessment. This part aims at methodology developments in two approaches. The first one is to develop model-free analysis method for DCE-MRI functional heterogeneity evaluation. This approach is inspired by the rationale that radiotherapy-induced functional change could be heterogeneous across the treatment area. The first effort was spent on a translational investigation of classic fractal dimension theory for DCE-MRI therapeutic response assessment. In a small-animal anti-angiogenesis drug therapy experiment, the randomly assigned treatment/control groups received multiple fraction treatments with one pre-treatment and multiple post-treatment high spatiotemporal DCE-MRI scans. In the post-treatment scan two weeks after the start, the investigated Rényi dimensions of the classic PK rate constant map demonstrated significant differences between the treatment and the control groups; when Rényi dimensions were adopted for treatment/control group classification, the achieved accuracy was higher than the accuracy from using conventional PK parameter statistics. Following this pilot work, two novel texture analysis methods were proposed. First, a new technique called Gray Level Local Power Matrix (GLLPM) was developed. It intends to solve the lack of temporal information and poor calculation efficiency of the commonly used Gray Level Co-Occurrence Matrix (GLCOM) techniques. In the same small animal experiment, the dynamic curves of Haralick texture features derived from the GLLPM had an overall better performance than the corresponding curves derived from current GLCOM techniques in treatment/control separation and classification. The second developed method is dynamic Fractal Signature Dissimilarity (FSD) analysis. Inspired by the classic fractal dimension theory, this method measures the dynamics of tumor heterogeneity during the contrast agent uptake in a quantitative fashion on DCE images. In the small animal experiment mentioned before, the selected parameters from dynamic FSD analysis showed significant differences between treatment/control groups as early as after 1 treatment fraction; in contrast, metrics from conventional PK analysis showed significant differences only after 3 treatment fractions. When using dynamic FSD parameters, the treatment/control group classification after 1st treatment fraction was improved than using conventional PK statistics. These results suggest the promising application of this novel method for capturing early therapeutic response.

The second approach of developing novel DCE-MRI methods is to combine PK information from multiple PK models. Currently, the classic Tofts model or its alternative version has been widely adopted for DCE-MRI analysis as a gold-standard approach for therapeutic response assessment. Previously, a shutter-speed (SS) model was proposed to incorporate transcytolemmal water exchange effect into contrast agent concentration quantification. In spite of richer biological assumption, its application in therapeutic response assessment is limited. It might be intriguing to combine the information from the SS model and from the classic Tofts model to explore potential new biological information for treatment assessment. The feasibility of this idea was investigated in the same small animal experiment. The SS model was compared against the Tofts model for therapeutic response assessment using PK parameter regional mean value comparison. Based on the modeled transcytolemmal water exchange rate, a biological subvolume was proposed and was automatically identified using histogram analysis. Within the biological subvolume, the PK rate constant derived from the SS model were proved to be superior to the one from Tofts model in treatment/control separation and classification. Furthermore, novel biomarkers were designed to integrate PK rate constants from these two models. When being evaluated in the biological subvolume, this biomarker was able to reflect significant treatment/control difference in both post-treatment evaluation. These results confirm the potential value of SS model as well as its combination with Tofts model for therapeutic response assessment.

In summary, this study addressed two problems of DCE-MRI application in radiotherapy assessment. In the first part, a method of accelerating DCE-MRI acquisition for better temporal resolution was investigated, and a novel PK model fitting algorithm was proposed for high temporal resolution DCE-MRI. In the second part, two model-free texture analysis methods and a multiple-model analysis method were developed for DCE-MRI therapeutic response assessment. The presented works could benefit the future DCE-MRI routine clinical application in radiotherapy assessment.

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Thermodynamic stability measurements on proteins and protein-ligand complexes can offer insights not only into the fundamental properties of protein folding reactions and protein functions, but also into the development of protein-directed therapeutic agents to combat disease. Conventional calorimetric or spectroscopic approaches for measuring protein stability typically require large amounts of purified protein. This requirement has precluded their use in proteomic applications. Stability of Proteins from Rates of Oxidation (SPROX) is a recently developed mass spectrometry-based approach for proteome-wide thermodynamic stability analysis. Since the proteomic coverage of SPROX is fundamentally limited by the detection of methionine-containing peptides, the use of tryptophan-containing peptides was investigated in this dissertation. A new SPROX-like protocol was developed that measured protein folding free energies using the denaturant dependence of the rate at which globally protected tryptophan and methionine residues are modified with dimethyl (2-hydroxyl-5-nitrobenzyl) sulfonium bromide and hydrogen peroxide, respectively. This so-called Hybrid protocol was applied to proteins in yeast and MCF-7 cell lysates and achieved a ~50% increase in proteomic coverage compared to probing only methionine-containing peptides. Subsequently, the Hybrid protocol was successfully utilized to identify and quantify both known and novel protein-ligand interactions in cell lysates. The ligands under study included the well-known Hsp90 inhibitor geldanamycin and the less well-understood omeprazole sulfide that inhibits liver-stage malaria. In addition to protein-small molecule interactions, protein-protein interactions involving Puf6 were investigated using the SPROX technique in comparative thermodynamic analyses performed on wild-type and Puf6-deletion yeast strains. A total of 39 proteins were detected as Puf6 targets and 36 of these targets were previously unknown to interact with Puf6. Finally, to facilitate the SPROX/Hybrid data analysis process and minimize human errors, a Bayesian algorithm was developed for transition midpoint assignment. In summary, the work in this dissertation expanded the scope of SPROX and evaluated the use of SPROX/Hybrid protocols for characterizing protein-ligand interactions in complex biological mixtures.

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Energy efficiency and user comfort have recently become priorities in the Facility Management (FM) sector. This has resulted in the use of innovative building components, such as thermal solar panels, heat pumps, etc., as they have potential to provide better performance, energy savings and increased user comfort. However, as the complexity of components increases, the requirement for maintenance management also increases. The standard routine for building maintenance is inspection which results in repairs or replacement when a fault is found. This routine leads to unnecessary inspections which have a cost with respect to downtime of a component and work hours. This research proposes an alternative routine: performing building maintenance at the point in time when the component is degrading and requires maintenance, thus reducing the frequency of unnecessary inspections. This thesis demonstrates that statistical techniques can be used as part of a maintenance management methodology to invoke maintenance before failure occurs. The proposed FM process is presented through a scenario utilising current Building Information Modelling (BIM) technology and innovative contractual and organisational models. This FM scenario supports a Degradation based Maintenance (DbM) scheduling methodology, implemented using two statistical techniques, Particle Filters (PFs) and Gaussian Processes (GPs). DbM consists of extracting and tracking a degradation metric for a component. Limits for the degradation metric are identified based on one of a number of proposed processes. These processes determine the limits based on the maturity of the historical information available. DbM is implemented for three case study components: a heat exchanger; a heat pump; and a set of bearings. The identified degradation points for each case study, from a PF, a GP and a hybrid (PF and GP combined) DbM implementation are assessed against known degradation points. The GP implementations are successful for all components. For the PF implementations, the results presented in this thesis find that the extracted metrics and limits identify degradation occurrences accurately for components which are in continuous operation. For components which have seasonal operational periods, the PF may wrongly identify degradation. The GP performs more robustly than the PF, but the PF, on average, results in fewer false positives. The hybrid implementations, which are a combination of GP and PF results, are successful for 2 of 3 case studies and are not affected by seasonal data. Overall, DbM is effectively applied for the three case study components. The accuracy of the implementations is dependant on the relationships modelled by the PF and GP, and on the type and quantity of data available. This novel maintenance process can improve equipment performance and reduce energy wastage from BSCs operation.

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Advanced Placement is a series of courses and tests designed to determine mastery over introductory college material. It has become part of the American educational system. The changing conception of AP was examined using critical theory to determine what led to a view of continual success. The study utilized David Armstrong’s variation of Michel Foucault’s critical theory to construct an analytical framework. Black and Ubbes’ data gathering techniques and Braun and Clark’s data analysis were utilized as the analytical framework. Data included 1135 documents: 641 journal articles, 421 newspaper articles and 82 government documents. The study revealed three historical ruptures correlated to three themes containing subthemes. The first rupture was the Sputnik launch in 1958. Its correlated theme was AP leading to school reform with subthemes of AP as reform for able students and AP’s gaining of acceptance from secondary schools and higher education. The second rupture was the Nation at Risk report published in 1983. Its correlated theme was AP’s shift in emphasis from the exam to the course with the subthemes of AP as a course, a shift in AP’s target population, using AP courses to promote equity, and AP courses modifying curricula. The passage of the No Child Left Behind Act of 2001 was the third rupture. Its correlated theme was AP as a means to narrow the achievement gap with the subthemes of AP as a college preparatory program and the shifting of AP to an open access program. The themes revealed a perception that progressively integrated the program into American education. The AP program changed emphasis from tests to curriculum, and is seen as the nation’s premier academic program to promote reform and prepare students for college. It has become a major source of income for the College Board. In effect, AP has become an agent of privatization, spurring other private entities into competition for government funding. The change and growth of the program over the past 57 years resulted in a deep integration into American education. As such the program remains an intrinsic part of the system and continues to evolve within American education.

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The necessity of elemental analysis techniques to solve forensic problems continues to expand as the samples collected from crime scenes grow in complexity. Laser ablation ICP-MS (LA-ICP-MS) has been shown to provide a high degree of discrimination between samples that originate from different sources. In the first part of this research, two laser ablation ICP-MS systems were compared, one using a nanosecond laser and another a femtosecond laser source for the forensic analysis of glass. The results showed that femtosecond LA-ICP-MS did not provide significant improvements in terms of accuracy, precision and discrimination, however femtosecond LA-ICP-MS did provide lower detection limits. In addition, it was determined that even for femtosecond LA-ICP-MS an internal standard should be utilized to obtain accurate analytical results for glass analyses. In the second part, a method using laser induced breakdown spectroscopy (LIBS) for the forensic analysis of glass was shown to provide excellent discrimination for a glass set consisting of 41 automotive fragments. The discrimination power was compared to two of the leading elemental analysis techniques, µXRF and LA-ICP-MS, and the results were similar; all methods generated >99% discrimination and the pairs found indistinguishable were similar. An extensive data analysis approach for LIBS glass analyses was developed to minimize Type I and II errors en route to a recommendation of 10 ratios to be used for glass comparisons. Finally, a LA-ICP-MS method for the qualitative analysis and discrimination of gel ink sources was developed and tested for a set of ink samples. In the first discrimination study, qualitative analysis was used to obtain 95.6% discrimination for a blind study consisting of 45 black gel ink samples provided by the United States Secret Service. A 0.4% false exclusion (Type I) error rate and a 3.9% false inclusion (Type II) error rate was obtained for this discrimination study. In the second discrimination study, 99% discrimination power was achieved for a black gel ink pen set consisting of 24 self collected samples. The two pairs found to be indistinguishable came from the same source of origin (the same manufacturer and type of pen purchased in different locations). It was also found that gel ink from the same pen, regardless of the age, was indistinguishable as were gel ink pens (four pens) originating from the same pack.

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Background There is increasing interest in how culture may affect the quality of healthcare services, and previous research has shown that ‘treatment culture’—of which there are three categories (resident centred, ambiguous and traditional)—in a nursing home may influence prescribing of psychoactive medications. Objective The objective of this study was to explore and understand treatment culture in prescribing of psychoactive medications for older people with dementia in nursing homes. Method Six nursing homes—two from each treatment culture category—participated in this study. Qualitative data were collected through semi-structured interviews with nursing home staff and general practitioners (GPs), which sought to determine participants’ views on prescribing and administration of psychoactive medication, and their understanding of treatment culture and its potential influence on prescribing of psychoactive drugs. Following verbatim transcription, the data were analysed and themes were identified, facilitated by NVivo and discussion within the research team. Results Interviews took place with five managers, seven nurses, 13 care assistants and two GPs. Four themes emerged: the characteristics of the setting, the characteristics of the individual, relationships and decision making. The characteristics of the setting were exemplified by views of the setting, daily routines and staff training. The characteristics of the individual were demonstrated by views on the personhood of residents and staff attitudes. Relationships varied between staff within and outside the home. These relationships appeared to influence decision making about prescribing of medications. The data analysis found that each home exhibited traits that were indicative of its respective assigned treatment culture. Conclusion Nursing home treatment culture appeared to be influenced by four main themes. Modification of these factors may lead to a shift in culture towards a more flexible, resident-centred culture and a reduction in prescribing and use of psychoactive medication. 

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Tide gauge data are identified as legacy data given the radical transition between observation method and required output format associated with tide gauges over the 20th-century. Observed water level variation through tide-gauge records is regarded as the only significant basis for determining recent historical variation (decade to century) in mean sea-level and storm surge. There are limited tide gauge records that cover the 20th century, such that the Belfast (UK) Harbour tide gauge would be a strategic long-term (110 years) record, if the full paper-based records (marigrams) were digitally restructured to allow for consistent data analysis. This paper presents the methodology of extracting a consistent time series of observed water levels from the 5 different Belfast Harbour tide gauges’ positions/machine types, starting late 1901. Tide-gauge data was digitally retrieved from the original analogue (daily) records by scanning the marigrams and then extracting the sequential tidal elevations with graph-line seeking software (Ungraph™). This automation of signal extraction allowed the full Belfast series to be retrieved quickly, relative to any manual x–y digitisation of the signal. Restructuring variably lengthed tidal data sets to a consistent daily, monthly and annual file format was undertaken by project-developed software: Merge&Convert and MergeHYD allow consistent water level sampling both at 60 min (past standard) and 10 min intervals, the latter enhancing surge measurement. Belfast tide-gauge data have been rectified, validated and quality controlled (IOC 2006 standards). The result is a consistent annual-based legacy data series for Belfast Harbour that includes over 2 million tidal-level data observations.

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Syria has been a major producer and exporter of fresh fruit and vegetables (FFV) in the Arabic region. Prior to 2011, Syrian FFV were mainly exported to the neighbouring countries, the Gulf States and Northern Africa as well as to Eastern European countries. Although the EU is potentially one of the most profitable markets of high quality FFV (such as organic ones) in the world, Syrian exports of FFV to Western European countries like Germany have been small. It could be a lucrative opportunity for Syrian growers and exporters of FFV to export organic products to markets such as Germany, where national production is limited to a few months due to climatic conditions. Yet, the organic sector in Syria is comparatively young and only a very small area of FFV is certified according to EU organic regulations. Up to the author’s knowledge, little was known about Syrian farmers’ attitudes towards organic FFV production. There was also no study so far that explored and analysed the determining factors for organic FFV adoption among Syrian farmers as well as the exports of these products to the EU markets. The overarching aim of the present dissertation focused on exploring and identifying the market potential of Syrian exports of organic FFV to Germany. The dissertation was therefore concerned with three main objectives: (i) to explore if German importers and wholesalers of organic FFV see market opportunities for Syrian organic products and what requirements in terms of quality and quantity they have, (ii) to determine the obstacles Syrian producers and exporters face when exporting agricultural products to Germany, and (iii) to investigate whether Syrian farmers of FFV can imagine converting their farms to organic production as well as the underlying reasons why they do so or not. A twofold methodological approach with expert interviews and a farmer survey were used in this dissertation to address the abovementioned objectives. While expert interviews were conducted with German and Syrian wholesalers of (organic) FFV in 2011 (9 interviews each), the farmer survey was administrated with 266 Syrian farmers of FFV in the main region for the production of FFV (i.e. the coastal region) from November 2012 till May 2013. For modelling farmers’ decisions to adopt organic farming, the Theory of Planned Behaviour as theoretical framework and Partial Least Squares Structural Equation Modelling as the main method for data analysis were used in this study. The findings of this dissertation yield implications for the different stakeholders (governmental institutions and NGOs, farmers, exporters, wholesalers, etc.) who are interested in prompting the Syrian export of organic products. Based on the empirical results and a literature review, an action plan to promote Syrian production and export of organic products was developed which can help in the post-war period in Syria at improving the organic sector.

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The Twitter System is the biggest social network in the world, and everyday millions of tweets are posted and talked about, expressing various views and opinions. A large variety of research activities have been conducted to study how the opinions can be clustered and analyzed, so that some tendencies can be uncovered. Due to the inherent weaknesses of the tweets - very short texts and very informal styles of writing - it is rather hard to make an investigation of tweet data analysis giving results with good performance and accuracy. In this paper, we intend to attack the problem from another aspect - using a two-layer structure to analyze the twitter data: LDA with topic map modelling. The experimental results demonstrate that this approach shows a progress in twitter data analysis. However, more experiments with this method are expected in order to ensure that the accurate analytic results can be maintained.

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Thesis (Ph.D.)--University of Washington, 2016-08

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Attention Deficit Hyperactivity Disorder (ADHD) is one the most prevalent of childhood diagnoses. There is limited research available from the perspective of the child or young person with ADHD. The current research explored how young people perceive ADHD. A secondary aim of the study was to explore to what extent they identify with ADHD. Five participants took part in this study. Their views were explored using semi-structured interviews guided by methods from Personal Construct Psychology. The data was analysed using Interpretative Phenomenological Analysis (IPA). Data analysis suggests that the young people’s views of ADHD are complex and, at times, contradictory. Four super-ordinate themes were identified: What is ADHD?, The role and impact of others on the experience of ADHD, Identity conflict and My relationship with ADHD. The young people’s contradictory views on ADHD are reflective of portrayals of ADHD in the media. A power imbalance was also identified where the young people perceive that they play a passive role in the management of their treatment. Finally, the young people’s accounts revealed a variety of approaches taken to make sense of their condition.