Stochastic Modeling of Reversible Biochemical Reaction-Diffusion Systems and High-Resolution Shock-Capturing Methods for Fluid Interfaces

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

Quantitative evaluation of visual function 12 months after bilateral implantation of a diffractive trifocal IOL

PURPOSE: To quantitatively evaluate visual function 12 months after bilateral implantation of the Physiol FineVision® trifocal intraocular lens (IOL) and to compare these results with those obtained in the first postoperative month. METHODS: In this prospective case series, 20 eyes of 10 consecutive patients were included. Monocular and binocular, uncorrected and corrected visual acuities (distance, near, and intermediate) were measured. Metrovision® was used to test contrast sensitivity under static and dynamic conditions, both in photopic and low-mesopic settings. The same software was used for pupillometry and glare evaluation. Motion, achromatic, and chromatic contrast discrimination were tested using 2 innovative psychophysical tests. A complete ophthalmologic examination was performed preoperatively and at 1, 3, 6, and 12 months postoperatively. Psychophysical tests were performed 1 month after surgery and repeated 12 months postoperatively. RESULTS: Final distance uncorrected visual acuity (VA) was 0.00 ± 0.08 and distance corrected VA was 0.00 ± 0.05 logMAR. Distance corrected near VA was 0.00 ± 0.09 and distance corrected intermediate VA was 0.00 ± 0.06 logMAR. Glare testing, pupillometry, contrast sensitivity, motion, and chromatic and achromatic contrast discrimination did not differ significantly between the first and last visit (p>0.05) or when compared to an age-matched control group (p>0.05). CONCLUSIONS: The Physiol FineVision® trifocal IOL provided satisfactory full range of vision and quality of vision parameters 12 months after surgery. Visual acuity and psychophysical tests did not vary significantly between the first and last visit.

RETINAL ANGIOMATOUS PROLIFERATION: A Quantitative Analysis of the Fundoscopic Features of the Fellow Eye

PURPOSE: To quantitatively analyze and compare the fundoscopic features between fellow eyes of retinal angiomatous proliferation and typical exudative age-related macular degeneration and to identify possible predictors of neovascularization. METHODS: Retrospective case-control study. Seventy-nine fellow eyes of unilateral retinal angiomatous proliferation (n = 40) and typical exudative age-related macular degeneration (n = 39) were included. Fundoscopic features of the fellow eyes were assessed using digital color fundus photographs taken at the time of diagnosis of neovascularization in the first affected eye. Grading was performed by two independent graders using RetmarkerAMD, a computer-assisted grading software based on the International Classification and Grading System for age-related macular degeneration. RESULTS: Baseline total number and area (square micrometers) of drusen in the central 1,000, 3,000, and 6,000 μm were considerably inferior in the fellow eyes of retinal angiomatous proliferation, with statistically significant differences (P < 0.05) observed in virtually every location (1,000, 3,000, and 6,000 μm). A soft drusen (≥125 μm) area >510,196 μm2 in the central 6,000 μm was associated with an increased risk of neovascularization (hazard ratio, 4.35; 95% confidence interval [1.56-12.15]; P = 0.005). CONCLUSION: Baseline fundoscopic features of the fellow eye differ significantly between retinal angiomatous proliferation and typical exudative age-related macular degeneration. A large area (>510,196 μm2) of soft drusen in the central 6,000 μm confers a significantly higher risk of neovascularization and should be considered as a phenotypic risk factor.

Assessing the Role of Vocabulary Breadth and Depth in Reading Comprehension: A Quantitative Study of Finnish EFL Learners

In this MA thesis, Finnish learners of English were studied in order to examine the relationship between second language vocabulary size, vocabulary depth, and reading comprehension. In addition, given the well-established connection between vocabulary size and reading comprehension, the second aim of the study was to see whether assessing vocabulary depth could add another dimension in predicting and explaining reading comprehension proficiency. Two groups were studied: the first group consisted of 39 Finnish upper secondary school students (the TOKA group) whereas the second group consisted of 19 university students of English at the University of Turku (the YLI group). Thus, comparisons were made between the results of a less advanced and a very advanced group of English learners, which was the third aim of the study. The participants in both groups filled in a background information form and took three tests: a multiple-choice reading comprehension test, a multiple-choice vocabulary size test, and a test designed to elicit information on learners’ depth of vocabulary knowledge of certain English words. The data were analysed using statistical methods. The results of the study show that the scores on the three tests were positively correlated in both study groups as well as in the two groups together. However, the correlations were higher in the TOKA group and in the two groups in total than in the YLI group. When examining the variance in reading comprehension test scores explained by vocabulary size and vocabulary depth, the figures of explained variance were again higher in the TOKA group and in the two groups in total than in the YLI group. When it comes to the results of the YLI group, vocabulary depth did not indeed seem to add any explained variance into the explanation of reading comprehension test scores. Based on the results of the study, it seems that vocabulary size and depth have a less significant role in the reading comprehension skills of more advanced learners of English. When looking at the less advanced TOKA group, on the other hand, vocabulary size and depth seem to be clear indicators of reading proficiency. In addition, the test results of the YLI group were clearly more uniform than those of the TOKA group. The variance in the test results of the TOKA group was large.

Grounded Theory methods in child psychotherapy research

This article considers the place of qualitative research in psychoanalysis and child psychotherapy. It discusses why research methodology for many years occupied so small a place in these fields, and examines the cultural and social developments since the 1960s which have changed this situation, giving formal methods of research much greater significance. It reflects on the different pressures to develop formal research methods which arise both from outside the psychoanalytic field, as a condition of its continued professional survival, and from within it, where its main aim is the development of fundamental psychoanalytic knowledge, It suggests that the conduct of mainly quantitative research into treatment outcomes is largely a response to these external pressures, whilst the main benefits to be gained from the development of qualitative research methods, such as Grounded Theory, are in facilitating the knowledge-generating capacities and achievements of child psychotherapists themselves. The paper describes Grounded Theory methods, and explains how they can be valuable in the recognition of hitherto unrecognised meanings and patterns as these are made visible in clinical practice. Finally, it briefly describes five different examples of completed doctoral studies, all of which have added significantly to the knowledge-base of child psychotherapy, and which demonstrate how much can be accomplished using this method of research.

Self-management of coronary heart disease in angina patients after percutaneous coronary intervention: A mixed methods study.

After having elective percutaneous coronary intervention (PCI) patients are expected to self-manage their coronary heart disease (CHD) by modifying their risk factors, adhering to medication and effectively managing any recurring angina symptoms but that may be ineffective. Objective: Explore how patients self-manage their coronary heart disease (CHD) after elective PCI and identify any factors that may infl uence that. Design and method: This mixed methods study recruited a convenience sample of patients (n=93) approximately three months after elective PCI. Quantitative data were collected using a survey and were subject to univariate, bivariate and multi-variate analysis. Qualitative data from participant interviews was analysed using thematic analysis. Findings: After PCI, 74% of participants managed their angina symptoms inappropriately. Younger participants and those with threatening perceptions of their CHD were more likely to know how to effectively manage their angina symptoms. Few patients adopted a healthier lifestyle after PCI. Qualitative analysis revealed that intentional non-adherence to some medicines was an issue. Some participants felt unsupported by healthcare providers and social networks in relation to their self-management. Participants reported strong emotional responses to CHD and this had a detrimental effect on their self-management. Few patients accessed cardiac rehabilitation.

Quantitative evaluation of visual function 12 months after bilateral implantation of a diffractive trifocal IOL

PURPOSE: To quantitatively evaluate visual function 12 months after bilateral implantation of the Physiol FineVision® trifocal intraocular lens (IOL) and to compare these results with those obtained in the first postoperative month. METHODS: In this prospective case series, 20 eyes of 10 consecutive patients were included. Monocular and binocular, uncorrected and corrected visual acuities (distance, near, and intermediate) were measured. Metrovision® was used to test contrast sensitivity under static and dynamic conditions, both in photopic and low-mesopic settings. The same software was used for pupillometry and glare evaluation. Motion, achromatic, and chromatic contrast discrimination were tested using 2 innovative psychophysical tests. A complete ophthalmologic examination was performed preoperatively and at 1, 3, 6, and 12 months postoperatively. Psychophysical tests were performed 1 month after surgery and repeated 12 months postoperatively. RESULTS: Final distance uncorrected visual acuity (VA) was 0.00 ± 0.08 and distance corrected VA was 0.00 ± 0.05 logMAR. Distance corrected near VA was 0.00 ± 0.09 and distance corrected intermediate VA was 0.00 ± 0.06 logMAR. Glare testing, pupillometry, contrast sensitivity, motion, and chromatic and achromatic contrast discrimination did not differ significantly between the first and last visit (p>0.05) or when compared to an age-matched control group (p>0.05). CONCLUSIONS: The Physiol FineVision® trifocal IOL provided satisfactory full range of vision and quality of vision parameters 12 months after surgery. Visual acuity and psychophysical tests did not vary significantly between the first and last visit.

RETINAL ANGIOMATOUS PROLIFERATION: A Quantitative Analysis of the Fundoscopic Features of the Fellow Eye

PURPOSE: To quantitatively analyze and compare the fundoscopic features between fellow eyes of retinal angiomatous proliferation and typical exudative age-related macular degeneration and to identify possible predictors of neovascularization. METHODS: Retrospective case-control study. Seventy-nine fellow eyes of unilateral retinal angiomatous proliferation (n = 40) and typical exudative age-related macular degeneration (n = 39) were included. Fundoscopic features of the fellow eyes were assessed using digital color fundus photographs taken at the time of diagnosis of neovascularization in the first affected eye. Grading was performed by two independent graders using RetmarkerAMD, a computer-assisted grading software based on the International Classification and Grading System for age-related macular degeneration. RESULTS: Baseline total number and area (square micrometers) of drusen in the central 1,000, 3,000, and 6,000 μm were considerably inferior in the fellow eyes of retinal angiomatous proliferation, with statistically significant differences (P < 0.05) observed in virtually every location (1,000, 3,000, and 6,000 μm). A soft drusen (≥125 μm) area >510,196 μm2 in the central 6,000 μm was associated with an increased risk of neovascularization (hazard ratio, 4.35; 95% confidence interval [1.56-12.15]; P = 0.005). CONCLUSION: Baseline fundoscopic features of the fellow eye differ significantly between retinal angiomatous proliferation and typical exudative age-related macular degeneration. A large area (>510,196 μm2) of soft drusen in the central 6,000 μm confers a significantly higher risk of neovascularization and should be considered as a phenotypic risk factor.

Working with Student Teachers: A Mixed Methods Study to Examine the Roles and Self-Identified Dispositions of Cooperating Teachers

A critical component of teacher education is the field experience during which candidates practice under the supervision of experienced teachers. Programs use the InTASC Standards to define the requisite knowledge, skills, and dispositions for teaching. Practicing teachers are familiar with the concepts of knowledge and skills, but they are less familiar with dispositions. Practicing teachers who mentor prospective teachers are underrepresented in the literature, but they are critical to teacher preparation. The research goals were to describe the self-identified dispositions of cooperating teachers, identify what cooperating teachers consider their role in preparing prospective teachers, and explain challenges that cooperating teachers face. Using a mixed methods design, I conducted a quantitative survey followed by a qualitative case study. When I compared survey and case study data, cooperating teachers report possessing InTASC critical dispositions described in Standard 2: Learning Differences, Standard 3: Learning Environments, and Standard 9: Professional Learning and Ethical Practice, but not Standard 6: Assessment and Standard 10: Leadership and Collaboration. Cooperating teachers assume the roles of modeler, mentor and advisor, and informal evaluator. They explain student teachers often lack skills and dispositions to assume full teaching responsibilities and recommend that universities better prepare candidates for classrooms. Cooperating teachers felt university evaluations were not relevant to teaching reality. I recommend modifying field experiences to increase the quantity and duration of classroom placements. I suggest further research to detail cooperating teacher dispositions, compare cooperating teachers who work with different universities, and determine if cooperating teacher dispositions influence student teacher dispositions.

Quantitative measurement using scanning thermal microscopy

This thesis reports on the development of quantitative measurement using micromachined scanning thermal microscopy (SThM) probes. These thermal probes employ a resistive element at their end, which can be used in passive or active modes. With the help of a review of SThM, the current issues and potentials associated with this technique are revealed. As a consequence of this understanding, several experimental and theoretical methods are discussed, which expand our understanding of these probes. The whole thesis can be summarized into three parts, one focusing on the thermal probe, one on probe-sample thermal interactions, and the third on heat transfer within the sample. In the first part, a series of experiments are demonstrated, aimed at characterizing the probe in its electrical and thermal properties, benefiting advanced probe design, and laying a fundamental base for quantifying the temperature of the probe. The second part focuses on two artifacts observed during the thermal scans – one induced by topography and the other by air conduction. Correspondingly, two devices, probing these artifacts, are developed. A topography-free sample, utilizing a pattern transfer technique, minimises topography-related artifacts that limited the reliability of SThM data; a controlled temperature ‘Johnson noise device’, with multiple-heater design, offers a uniform, accurate, temperature distribution. Analyzing results of scan from these samples provides data for studying the thermal interactions within the probe and the tip-sample interface. In the final part, the observation is presented that quantification of measurements depends not only on an accurate measurement tool, but also on a deep understanding of the heat transfer within the sample resulting from the nanoscopic contact. It is believed that work in this thesis contributes to SThM gaining wider application in the scientific community.

Do Children's Health Resources Differ According to Preschool Physical Activity Programmes and Parental Behaviour? A Mixed Methods Study

Preschool can have positive effects on the development of a healthy lifestyle. The present study analysed to what extent different conditions, structures and behavioural models in preschool and family-children's central social microsystems-can lead to differences in children's health resources. Using a cross-sectional mixed methods approach, contrast analyses of "preschools with systematic physical activity programmes" versus "preschools without physical activity programmes" were conducted to assess the extent to which children's physical activity, quality of life and social behaviour differ between preschools with systematic and preschools without physical activity programmes. Differences in children's physical activity according to parental behaviour were likewise assessed. Data on child-related outcomes and parent-related factors were collected via parent questionnaires and child interviews. A qualitative focused ethnographic study was performed to obtain deeper insight into the quantitative survey data. Two hundred and twenty seven (227) children were interviewed at 21 preschools with systematic physical activity programmes, and 190 at 25 preschools without physical activity programmes. There was no significant difference in children's physical activity levels between the two preschool types (p = 0.709). However, the qualitative data showed differences in the design and quality of programmes to promote children's physical activity. Data triangulation revealed a strong influence of parental behaviour. The triangulation of methods provided comprehensive insight into the nature and extent of physical activity programmes in preschools and made it possible to capture the associations between systematic physical activity promotion and children's health resources in a differential manner.

Mindfulness-Based Cognitive Therapy for older people in a community setting: a mixed methods feasibility study

Rationale: In line with complex intervention development, this research takes a systematic approach to examining the feasibility and acceptability of delivering Mindfulness-Based Cognitive Therapy (MBCT) to older people who experience symptoms of depression. Methods: A mixed methods approach was adopted in line with recommendations made by the MRC Complex Intervention Development framework. Quantitative and qualitative methods were combined by administering questionnaires as well as conducting post intervention interviews. A number of trial feasibility factors were examined such as recruitment and attrition rates. Qualitative data was analysed using Braun and Clarke’s thematic analysis framework. Results: Nine participants started the MBCT intervention and six completed the 8-week programme. The results suggest that MBCT for older people is feasible and acceptable. Participants reported improved mindfulness skills. Participants responded positively to being asked to take part in research and appeared to particularly value the group delivery format of the intervention. Conclusions: MBCT is both feasible and acceptable for older people experiencing symptoms of depression. Further research is required with larger sample sizes to allow for more robust statistical exploration of outcome measures, including mechanisms of change.

Tissue Proteomes: Quantitative Mass Spectrometry of Murine Liver and Ovarian Endometrioma

A human genome contains more than 20 000 protein-encoding genes. A human proteome, instead, has been estimated to be much more complex and dynamic. The most powerful tool to study proteins today is mass spectrometry (MS). MS based proteomics is based on the measurement of the masses of charged peptide ions in a gas-phase. The peptide amino acid sequence can be deduced, and matching proteins can be found, using software to correlate MS-data with sequence database information. Quantitative proteomics allow the estimation of the absolute or relative abundance of a certain protein in a sample. The label-free quantification methods use the intrinsic MS-peptide signals in the calculation of the quantitative values enabling the comparison of peptide signals from numerous patient samples. In this work, a quantitative MS methodology was established to study aromatase overexpressing (AROM+) male mouse liver and ovarian endometriosis tissue samples. The workflow of label-free quantitative proteomics was optimized in terms of sensitivity and robustness, allowing the quantification of 1500 proteins with a low coefficient of variance in both sample types. Additionally, five statistical methods were evaluated for the use with label-free quantitative proteomics data. The proteome data was integrated with other omics datasets, such as mRNA microarray and metabolite data sets. As a result, an altered lipid metabolism in liver was discovered in male AROM+ mice. The results suggest a reduced beta oxidation of long chain phospholipids in the liver and increased levels of pro-inflammatory fatty acids in the circulation in these mice. Conversely, in the endometriosis tissues, a set of proteins highly specific for ovarian endometrioma were discovered, many of which were under the regulation of the growth factor TGF-β1. This finding supports subsequent biomarker verification in a larger number of endometriosis patient samples.

A comparison of neck bending and flexion measurement methods for assessment of ergonomic risk

International audience

Mapping tissue inhomogeneity in acute myocarditis: a novel analytical approach to quantitative myocardial edema imaging by T2-mapping

BACKGROUND: The purpose of the present study was to investigate the diagnostic value of T2-mapping in acute myocarditis (ACM) and to define cut-off values for edema detection. METHODS: Cardiovascular magnetic resonance (CMR) data of 31 patients with ACM were retrospectively analyzed. 30 healthy volunteers (HV) served as a control. Additionally to the routine CMR protocol, T2-mapping data were acquired at 1.5 T using a breathhold Gradient-Spin-Echo T2-mapping sequence in six short axis slices. T2-maps were segmented according to the 16-segments AHA-model and segmental T2 values as well as the segmental pixel-standard deviation (SD) were analyzed. RESULTS: Mean differences of global myocardial T2 or pixel-SD between HV and ACM patients were only small, lying in the normal range of HV. In contrast, variation of segmental T2 values and pixel-SD was much larger in ACM patients compared to HV. In random forests and multiple logistic regression analyses, the combination of the highest segmental T2 value within each patient (maxT2) and the mean absolute deviation (MAD) of log-transformed pixel-SD (madSD) over all 16 segments within each patient proved to be the best discriminators between HV and ACM patients with an AUC of 0.85 in ROC-analysis. In classification trees, a combined cut-off of 0.22 for madSD and of 68 ms for maxT2 resulted in 83% specificity and 81% sensitivity for detection of ACM. CONCLUSIONS: The proposed cut-off values for maxT2 and madSD in the setting of ACM allow edema detection with high sensitivity and specificity and therefore have the potential to overcome the hurdles of T2-mapping for its integration into clinical routine.