Essays on Machine Learning and Hedonic Models

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

Implementation science to expand an mHealth intervention for improving retention in care for women living with HIV and their children

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

Alternative approaches to education: Tolstoy’s thinking on teaching and learning and its relevance for today

In this article I reflect upon the educational writings and teaching experiences of the 19th-Century Russian novelist Leo Tolstoy. Tolstoy is known to have attached much importance to his own writing on education, even more than to the literary creations for which he is best remembered. His writings on education have much to contribute to our present-day understanding of the learning process and cover such issues as, ‘learner autonomy’, ‘motivation’, ‘relationship’ and ‘student voice’. Tolstoy’s teaching experience was with multiethnic peasant children in his schools in Yasnaya Polyana. I intend to illustrate that the themes and issues that arose from his experiences in the 1860s can still find resonance with students and teachers in the 21st century.

Peer Relationships in School-Age Children with Autism: Concurrent and Longitudinal Predictors

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

Human Ezrin: Prediction of the 3D structure and interactions with mTOR

The protein Ezrin, is a member of the ERM family (Ezrin, Radixin and Moesin) that links the F-actin to the plasma membrane. The protein is made of three domains namely the FERM domain, a central α-helical domain and the CERMAD domain. The residues in Ezrin such as Ser66, Tyr145, Tyr353 and Tyr477 regulate the function of the protein through phosphorylation. The protein is found in two distinct conformations of active and dormant (inactive) state. The initial step during the conformation change is the breakage of intramolecular interaction in dormant Ezrin by phosphorylation of residue Thr567. The dormant structure of human Ezrin was predicted computationally since only partial active form structure was available. The validation analysis showed that 99.7% residues were positioned in favored, allowed and generously allowed regions of the Ramachandran plot. The Z-score of Ezrin was −7.36, G-factor was 0.1, and the QMEAN score of the model was 0.61 indicating a good model for human Ezrin. The comparison of the conformations of the activated and dormant Ezrin showed a major shift in the F2 lobe (residues 142-149 and 161-177) while changes in the conformation induced mobility shifts in lobe F3 (residues 261 to 267). The 3D positions of the phosphorylation sites Tyr145, Tyr353, Tyr477, Tyr482 and Thr567 were also located. Using targeted molecular dynamic simulation, the molecular movements during conformational change from active to dormant were visualized. The dormant Ezrin auto-inhibits itself by a head-to-tail interaction of the N-terminal and C-terminal residues. The trajectory shows the breakage of the interactions and mobility of the CERMAD domain away from the FERM domain. Protein docking and clustering analysis were used to predict the residues involved in the interaction between dormant Ezrin and mTOR. Residues Tyr477 and Tyr482 were found to be involved in interaction with mTOR.

Dilemas éticos en niños con enfermedades neuromusculares y dependencias tecnológicas: Ethical dilemmas in children with neuromuscular diseases and technological dependencies

En los últimos años, los cuidados respiratorios especializados, y en particular los cuidados respiratorios no invasivos y otros avances tecnológicos han contribuido a una mejor calidad de vida y sobrevida de los pacientes con enfermedades neuromusculares. La naturaleza de las opciones terapéuticas (como ser la ventilación invasiva versus ventilación no invasiva, las cargas psicológicas, sociales y financieras) tienen ramificaciones éticas. Por lo tanto resulta esencial que los médicos comprendan todas las opciones terapéuticas y los factores psicosociales al informar a sus pacientes, en lo que tiene que ver con sus ventajas y desventajas y sus costos asociados, de modo que los padres puedan tomar decisiones informadas. Los nuevos desarrollos incluyen exámenes prenatales y neonatales más precisos, nuevas terapias genéticas y soporte respiratorio no invasivo para evitar episodios de fallas respiratorias y vías aéreas invasivas. Al empoderar a los pacientes y sus familias para educar y capacitar servicios personales de cuidados para que no deban depender de las instituciones y servicios de enfermería constante, y los recientes avances tecnológicos facilitan su permanencia en el hogar y dejan de estar atados a una vida dependiendo de la institución y los servicios de enfermería. Estos últimos infantilizan a los pacientes en lugar de promover su autonomía. Las consideraciones financieras, las terapias genéticas, el screening prenatal y las distintas opciones terapéuticas que promueven la autonomía, todos tienen implicancias éticas. Algunos de los avances discutidos en este artículo requieren un cambio de paradigma en la forma en que los médicos ven y tratan a estos individuos.

Datasets, features, learning, and models in visual recognition

Visual recognition is a fundamental research topic in computer vision. This dissertation explores datasets, features, learning, and models used for visual recognition. In order to train visual models and evaluate different recognition algorithms, this dissertation develops an approach to collect object image datasets on web pages using an analysis of text around the image and of image appearance. This method exploits established online knowledge resources (Wikipedia pages for text; Flickr and Caltech data sets for images). The resources provide rich text and object appearance information. This dissertation describes results on two datasets. The first is Berg’s collection of 10 animal categories; on this dataset, we significantly outperform previous approaches. On an additional set of 5 categories, experimental results show the effectiveness of the method. Images are represented as features for visual recognition. This dissertation introduces a text-based image feature and demonstrates that it consistently improves performance on hard object classification problems. The feature is built using an auxiliary dataset of images annotated with tags, downloaded from the Internet. Image tags are noisy. The method obtains the text features of an unannotated image from the tags of its k-nearest neighbors in this auxiliary collection. A visual classifier presented with an object viewed under novel circumstances (say, a new viewing direction) must rely on its visual examples. This text feature may not change, because the auxiliary dataset likely contains a similar picture. While the tags associated with images are noisy, they are more stable when appearance changes. The performance of this feature is tested using PASCAL VOC 2006 and 2007 datasets. This feature performs well; it consistently improves the performance of visual object classifiers, and is particularly effective when the training dataset is small. With more and more collected training data, computational cost becomes a bottleneck, especially when training sophisticated classifiers such as kernelized SVM. This dissertation proposes a fast training algorithm called Stochastic Intersection Kernel Machine (SIKMA). This proposed training method will be useful for many vision problems, as it can produce a kernel classifier that is more accurate than a linear classifier, and can be trained on tens of thousands of examples in two minutes. It processes training examples one by one in a sequence, so memory cost is no longer the bottleneck to process large scale datasets. This dissertation applies this approach to train classifiers of Flickr groups with many group training examples. The resulting Flickr group prediction scores can be used to measure image similarity between two images. Experimental results on the Corel dataset and a PASCAL VOC dataset show the learned Flickr features perform better on image matching, retrieval, and classification than conventional visual features. Visual models are usually trained to best separate positive and negative training examples. However, when recognizing a large number of object categories, there may not be enough training examples for most objects, due to the intrinsic long-tailed distribution of objects in the real world. This dissertation proposes an approach to use comparative object similarity. The key insight is that, given a set of object categories which are similar and a set of categories which are dissimilar, a good object model should respond more strongly to examples from similar categories than to examples from dissimilar categories. This dissertation develops a regularized kernel machine algorithm to use this category dependent similarity regularization. Experiments on hundreds of categories show that our method can make significant improvement for categories with few or even no positive examples.

Understanding and validating accelerometry as a measure of physical activity in children with intellectual disabilities

Background Physical activity in children with intellectual disabilities is a neglected area of study, which is most apparent in relation to physical activity measurement research. Although objective measures, specifically accelerometers, are widely used in research involving children with intellectual disabilities, existing research is based on measurement methods and data interpretation techniques generalised from typically developing children. However, due to physiological and biomechanical differences between these populations, questions have been raised in the existing literature on the validity of generalising data interpretation techniques from typically developing children to children with intellectual disabilities. Therefore, there is a need to conduct population-specific measurement research for children with intellectual disabilities and develop valid methods to interpret accelerometer data, which will increase our understanding of physical activity in this population. Methods Study 1: A systematic review was initially conducted to increase the knowledge base on how accelerometers were used within existing physical activity research involving children with intellectual disabilities and to identify important areas for future research. A systematic search strategy was used to identify relevant articles which used accelerometry-based monitors to quantify activity levels in ambulatory children with intellectual disabilities. Based on best practice guidelines, a novel form was developed to extract data based on 17 research components of accelerometer use. Accelerometer use in relation to best practice guidelines was calculated using percentage scores on a study-by-study and component-by-component basis. Study 2: To investigate the effect of data interpretation methods on the estimation of physical activity intensity in children with intellectual disabilities, a secondary data analysis was conducted. Nine existing sets of child-specific ActiGraph intensity cut points were applied to accelerometer data collected from 10 children with intellectual disabilities during an activity session. Four one-way repeated measures ANOVAs were used to examine differences in estimated time spent in sedentary, moderate, vigorous, and moderate to vigorous intensity activity. Post-hoc pairwise comparisons with Bonferroni adjustments were additionally used to identify where significant differences occurred. Study 3: The feasibility on a laboratory-based calibration protocol developed for typically developing children was investigated in children with intellectual disabilities. Specifically, the feasibility of activities, measurements, and recruitment was investigated. Five children with intellectual disabilities and five typically developing children participated in 14 treadmill-based and free-living activities. In addition, resting energy expenditure was measured and a treadmill-based graded exercise test was used to assess cardiorespiratory fitness. Breath-by-breath respiratory gas exchange and accelerometry were continually measured during all activities. Feasibility was assessed using observations, activity completion rates, and respiratory data. Study 4: Thirty-six children with intellectual disabilities participated in a semi-structured school-based physical activity session to calibrate accelerometry for the estimation of physical activity intensity. Participants wore a hip-mounted ActiGraph wGT3X+ accelerometer, with direct observation (SOFIT) used as the criterion measure. Receiver operating characteristic curve analyses were conducted to determine the optimal accelerometer cut points for sedentary, moderate, and vigorous intensity physical activity. Study 5: To cross-validate the calibrated cut points and compare classification accuracy with existing cut points developed in typically developing children, a sub-sample of 14 children with intellectual disabilities who participated in the school-based sessions, as described in Study 4, were included in this study. To examine the validity, classification agreement was investigated between the criterion measure of SOFIT and each set of cut points using sensitivity, specificity, total agreement, and Cohen’s kappa scores. Results Study 1: Ten full text articles were included in this review. The percentage of review criteria met ranged from 12%−47%. Various methods of accelerometer use were reported, with most use decisions not based on population-specific research. A lack of measurement research, specifically the calibration/validation of accelerometers for children with intellectual disabilities, is limiting the ability of researchers to make appropriate and valid accelerometer use decisions. Study 2: The choice of cut points had significant and clinically meaningful effects on the estimation of physical activity intensity and sedentary behaviour. For the 71-minute session, estimations for time spent in each intensity between cut points ranged from: sedentary = 9.50 (± 4.97) to 31.90 (± 6.77) minutes; moderate = 8.10 (± 4.07) to 40.40 (± 5.74) minutes; vigorous = 0.00 (± .00) to 17.40 (± 6.54) minutes; and moderate to vigorous = 8.80 (± 4.64) to 46.50 (± 6.02) minutes. Study 3: All typically developing participants and one participant with intellectual disabilities completed the protocol. No participant met the maximal criteria for the graded exercise test or attained a steady state during the resting measurements. Limitations were identified with the usability of respiratory gas exchange equipment and the validity of measurements. The school-based recruitment strategy was not effective, with a participation rate of 6%. Therefore, a laboratory-based calibration protocol was not feasible for children with intellectual disabilities. Study 4: The optimal vertical axis cut points (cpm) were ≤ 507 (sedentary), 1008−2300 (moderate), and ≥ 2301 (vigorous). Sensitivity scores ranged from 81−88%, specificity 81−85%, and AUC .87−.94. The optimal vector magnitude cut points (cpm) were ≤ 1863 (sedentary), ≥ 2610 (moderate) and ≥ 4215 (vigorous). Sensitivity scores ranged from 80−86%, specificity 77−82%, and AUC .86−.92. Therefore, the vertical axis cut points provide a higher level of accuracy in comparison to the vector magnitude cut points. Study 5: Substantial to excellent classification agreement was found for the calibrated cut points. The calibrated sedentary cut point (ĸ =.66) provided comparable classification agreement with existing cut points (ĸ =.55−.67). However, the existing moderate and vigorous cut points demonstrated low sensitivity (0.33−33.33% and 1.33−53.00%, respectively) and disproportionately high specificity (75.44−.98.12% and 94.61−100.00%, respectively), indicating that cut points developed in typically developing children are too high to accurately classify physical activity intensity in children with intellectual disabilities. Conclusions The studies reported in this thesis are the first to calibrate and validate accelerometry for the estimation of physical activity intensity in children with intellectual disabilities. In comparison with typically developing children, children with intellectual disabilities require lower cut points for the classification of moderate and vigorous intensity activity. Therefore, generalising existing cut points to children with intellectual disabilities will underestimate physical activity and introduce systematic measurement error, which could be a contributing factor to the low levels of physical activity reported for children with intellectual disabilities in previous research.

FAMILY CHARACTERISTICS, STATE PROGRAM EFFECTIVENESS, AND REPORT OF INADEQUATE CARE AMONG FAMILIES OF YOUNG CHILDREN WITH HEARING LOSS

Approximately 1.6 per 1,000 newborns in the U.S. are born with hearing loss. Congenital hearing loss poses a risk to their speech, language, cognitive, and social-emotional development. Early detection and intervention can improve outcomes. Every state has an Early Hearing Detection and Intervention program (EHDI) to promote and track screening, audiological assessments and linkage to early intervention. However, a large percentage of children are “lost to system (LTS),” meaning that they did not receive recommended care or that it was not reported. This study used data from the 2009-2010 National Survey of Children with Special Health Care Needs and data from the 2011 EHDI Hearing Screening and Follow-Up Survey to examine how 1) family characteristics; 2) EHDI program effectiveness, as determined by LTS percentages; and 3) the family conditions of education and poverty are related to parental report of inadequate care. The sample comprised 684 children between the ages of 0 and 5 years with hearing loss. The results indicated that living in states with less effective EHDI programs was associated with an increased likelihood of not receiving early intervention services (EIS) and of reporting poor family-centered communication. Sibling classification was associated with both receipt of EIS and report of unmet need. Single mothers were less likely to report increased difficulties accessing care. Poor and less educated families, assessed separately, who lived in states with less effective EHDI programs, were more likely to report non-receipt of EIS and less likely to report unmet need as compared to similar families living in states with more effective programs. Poor families living in states with less effective programs were more likely to report less coordinated care than were poor families living in states with more effective programs. This study supports the conclusion that both family characteristics and the effectiveness of state programs affect quality of care outcomes. It appears that less effective state programs affect disadvantaged families’ service receipt report more than that of advantaged families. These findings are important because they may provide insights into the development of targeted efforts to improve the system of care for children with hearing loss.

Plain reasons why neither Dr. Watts' Imitations of the Psalms, nor his other poems, nor any other human composition, ought to be used in the praises of the great God our Saviour--but, that a metre version of the book of Psalms, examined, with wise and critical care by pious and learned divines, and found by them to be as near the Hebrew metre Psalms, as the idiom of the English language would admit, ought to be used.

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Metodologia participativa para repositórios de recursos educacionais abertos

This research deals with the use of a participatory design methodology to develop a repository of open educational resources, the Arcaz. Discusses key aspects of neutrality and determinism of technology within the context of Social Studies of Science and Technology and presents some concepts of critical theory of technology related to the democratic construction of technological artifacts. Discusses the philosophical heritage of the movements that led to the emergence of free software, open education and open educational resources and argues that participatory design share similar ideals. It presents concepts of human-computer interaction, interaction design and user centered design, important to enhance the user experience in information systems. It addresses the participatory design as a methodology that allows the democratic participation of users in the technological construction, promoting mutual learning and active voice for the participants. Develops a participatory design methodology adapted to the Arcaz context of use and provides the procedures for the meetings conducted to apply participatory design techniques to the repository and the results obtained. It concludes with a study of some of the interventions suggested in the system and orientations for future applications of participatory practices in the development of the repository and a list of best practices, focusing on ethical principles that should guide the participatory design.

Effect of vitamin D supplementation on bone status, glucose homeostasis and immune function in children with vitamin D deficiency

Background: Between 1961-1971 vitamin D deficiency was recognized as a public health issue in the UK, because of the lack of effective sunlight and the population mix [1, 2]. In recent years, health care professionals have cited evidence suggesting a re-emergence of the vitamin D deficiency linked to a number of health consequences as a concern [3-6]. Evidence from observational studies has linked low vitamin D status with impairment in glucose homeostasis and immune dysfunction [7-9]. However, interventional studies, particularly those focused on paediatric populations, have been limited and inconsistent. There is a need for detailed studies, to clarify the therapeutic benefits of vitamin D in these important clinical areas. Objective: The aims of this PhD thesis were two-fold. Firstly, to perform preliminary work assessing the association between vitamin D deficiency and bone status, glucose homeostasis and immune function, and to explore any changes in these parameters following short term vitamin D3 replacement therapy. Secondly, to assess the effectiveness of an electronic surveillance system (ScotPSU) as a tool to determine the current incidence of hospital-based presentation of childhood vitamin D deficiency in Scotland. Methods: Active surveillance was performed for a period of two years as a part of an electronic web-based surveillance programme performed by the Scottish Paediatric Surveillance Unit (ScotPSU). The validity of the system was assessed by identifying cases with profound vitamin D deficiency (in Glasgow and Edinburgh) from the regional laboratory. All clinical details were checked against those identified using the surveillance system. Thirty-seven children aged 3 months to 10 years, who had been diagnosed with vitamin D deficiency, were recruited for the bone, glucose and immunity studies over a period of 24 months. Twenty-five samples were analysed for the glucose and bone studies; of these, 18 samples were further analysed for immune study. Treatment consisted of six weeks taking 5000 IU units cholecalciferol orally once a day. At baseline and after completion of treatment, 25 hydroxyvitamin D (25(OH)D), parathyroid hormone (PTH), alkaline phosphatase (ALP), collagen type 1 cross-linked C-telopeptide (CTX), osteocalcin (OCN), calcium, phosphate, insulin, glucose, homeostasis model assessment index, estimated insulin resistance (HOMA IR), glycated hemoglobin (HbA1c), sex hormone binding globulin (SHBG), lipids profiles, T helper 1 (Th1) cytokines (interleukin-2 ( IL-2), tumor necrosis factors-alpha (TNF-α), interferon-gamma (INF-γ)), T helper 2 (Th2) cytokines (interleukin-4 (IL-4), interleukin-5 (IL-5), interleukin-6 (IL-6)), T helper 17 (Th17) cytokine (interleukin-17 (IL-17)), Regulatory T (Treg) cytokine (interleukin-10 (IL-10)) and chemokines/cytokines, linked with Th1/Th2 subset balance and/or differentiation (interleukin-8 (IL-8), interleukin-12 (IL-12), eosinophil chemotactic protein ( EOTAXIN), macrophage inflammatory proteins-1beta (MIP-1β), interferon-gamma-induced protein-10 (IP-10), regulated on activation, normal T cell expressed and secreted (RANTES), monocyte chemoattractant protein-1(MCP-1)) were measured. Leukoocyte subset analysis was performed for T cells, B cells and T regulatory cells and a luminex assay was used to measure the cytokiens. Results: Between September 2009 and August 2011, 163 cases of vitamin D deficiency were brought to the attention of the ScotPSU, and the majority of cases (n = 82) were reported in Glasgow. The cross-validation checking in Glasgow and Edinburgh over a one-year period revealed only 3 (11%) cases of clearly symptomatic vitamin D deficiency, which had been missed by the ScotPSU survey in Glasgow. While 16 (67%) symptomatic cases had failed to be reported through the ScotPSU survey in Edinburgh. For the 23 children who are included in bone and glucose studies, 22 (96%) children had basal serum 25(OH)D in the deficiency range (< 50 nmol/l) and one (4%) child had serum 25(OH)D in the insufficiency range (51-75 nmol/l). Following vitamin D3 treatment, 2 (9%) children had final serum 25(OH)D lower than 50 nmol/l, 6 (26%) children had final serum 25(OH)D between >50-75 nmol/l, 12 (52%) children reached a final serum 25(OH)D >75-150 nmol/l and finally 3 (13%) exceeded the normal reference range with a final 25(OH)D >150 nmol/l. Markers for remodelling ALP and PTH had significantly decreased (p = 0.001 and <0.0001 for ALP and PTH respectively). In 17 patients for whom insulin and HOMA IR data were available and enrolled in glucose study, significant improvements in insulin resistance (p = 0.04) with a trend toward a reduction in serum insulin (p = 0.05) was observed. Of those 14 children who had their cytokines profile data analysed and enrolled in the immunity study, insulin and HOMA IR data were missed in one child. A significant increase in the main Th2 secreted cytokine IL-4 (p = 0.001) and a tendency for significant increases in other Th2 secreted cytokines IL-5 (p = 0.05) and IL-6 (p = 0.05) was observed following vitamin D3 supplementation. Conclusion: An electronic surveillance system can provide data for studying the epidemiology of vitamin D deficiency. However, it may underestimate the number of positive cases. Improving vitamin D status in vitamin D deficient otherwise healthy children significantly improved their vitamin D deficient status, and was associated with an improvement in bone profile, improvements in insulin resistance and an alteration in main Th2 secreting cytokines.

Experiences of care and adjustment to change in caregivers of children with autoimmune encephalitis: an interpretative phenomenological analysis

Background: Autoimmune encephalitis (AE) occurs in response to an antibody-mediated central nervous system disease and can lead to significant neurodisability. Prior research on family adjustment has described a reciprocal relationship between caregiver functioning, distress and clinical outcome in parents and children with encephalitis. There has been no previous research exploring the experiences of caregivers with a child with AE. Aims: To explore the perspectives of parents and/or caregivers with a child diagnosed with AE regarding (i) their own adjustment from hospital admission to post-discharge, and (ii) their experiences of care and service provision. Methods: A purposive sampling approach was used. Five parents of children with AE participated in a semi-structured interview exploring their experiences of caring for their child and service provision during acute care and post-discharge. Interpretative Phenomenological Analysis (IPA) was used to analyse the transcripts. Main findings and conclusions: Four shared super-ordinate themes with related subthemes emerged: (a) uncertainty, (b) managing our recovery, (c) changes in my child, (d) experiences of service provision. Participants reported emotional distress, often underpinned by recurrent experiences of uncertainty, and ‘loss’ of the previous child, and mediated by coping strategies and social support. While an overall positive experience of inpatient services was reported, parents often perceived post-discharge services as lacking in co-ordination, communication and formal follow-up, resulting in unmet support needs. Implications and recommendations for services, practitioners and future research are discussed.

Does prenatal diagnosis modify neonatal treatment and early outcome of children with esophageal atresia?

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