Global properties of the mapping between local amino acid sequence and local structure in proteins.

Local protein structure prediction efforts have consistently failed to exceed approximately 70% accuracy. We characterize the degeneracy of the mapping from local sequence to local structure responsible for this failure by investigating the extent to which similar sequence segments found in different proteins adopt similar three-dimensional structures. Sequence segments 3-15 residues in length from 154 different protein families are partitioned into neighborhoods containing segments with similar sequences using cluster analysis. The consistency of the sequence-to-structure mapping is assessed by comparing the local structures adopted by sequence segments in the same neighborhood in proteins of known structure. In the 154 families, 45% and 28% of the positions occur in neighborhoods in which one and two local structures predominate, respectively. The sequence patterns that characterize the neighborhoods in the first class probably include virtually all of the short sequence motifs in proteins that consistently occur in a particular local structure. These patterns, many of which occur in transitions between secondary structural elements, are an interesting combination of previously studied and novel motifs. The identification of sequence patterns that consistently occur in one or a small number of local structures in proteins should contribute to the prediction of protein structure from sequence.

Harnessing Natural Resources for Development: New Legal Regimes for Localized Benefit Sharing in the Mining Sector

Thesis (Ph.D.)--University of Washington, 2016-06

Multimodal Transportation in Northeast Seattle: An Integrated Design

Thesis (Master's)--University of Washington, 2016-06

Sympathetic inhibition of accommodation after sustained nearwork in subjects with myopia and emmetropia

PURPOSE. The purposes of the present study were to assess the effect of a sympathetic inhibitory pharmacologic agent, timolol maleate, on the magnitude of nearwork-induced transient myopia (NITM) and its decay in different refractive groups for an extended near task duration and to determine the proportion of the young adult population manifesting effective sympathetic access under naturalistic closed-loop viewing conditions. METHODS. Ten subjects with emmetropia and 10 with myopia were tested. They read binocularly for 1 hour at a distance of 35 to 40 cm. NITM was calculated as the difference in distance refractive state after task as compared with before task immediately after reading. All subjects received timolol maleate to block the sympathetic nervous system and betaxolol as a control agent in independent test sessions separated by at least 3 days. Forty minutes after drug instillation, the NITM measurement procedure was repeated. RESULTS. Initial NITM magnitude was larger in subjects with myopia than in subjects with emmetropia before and after timolol instillation. Furthermore, NITM magnitude in subjects with sympathetic access was increased after timolol instillation. In contrast, with the control agent betaxolol, there was no increase. NITM decay duration to baseline was increased after timolol instillation in the subjects with myopia only. Only 15% of the subjects (n = 3 subjects with myopia) demonstrated effective and significant access to sympathetic facility. CONCLUSIONS. Subjects with myopia demonstrated an increase in decay duration with timolol, thus suggesting impaired sympathetic inhibition of accommodation. This may be a precursor for myopia progression in some persons.

Research with in-built replications:comment and further suggestions for replication research

This brief commentary on the paper Designing Research with In-built Differentiated Replication expands on concerns about a lack of replication research by focusing on three key questions of continuous importance: Why should researchers conduct more replication research? Why do so few researchers conduct replication studies? What can researchers do to add more studies? This paper identifies barriers preventing replication related to the scientific system, the replication researcher, and the initial research. Suggestions include publishing all papers electronically along with reviews; authors taking steps to encourage replications of their work; and editors inviting replications of important papers. The scientific community should establish a replication index as a measure of output quality. © 2012 Elsevier Inc.

Rebirth of a neighborhood: In streetscape design

This study involves one of the eight neighborhoods in the City of Miami named Little Havana. Little Havana, once a flourishing Hispanic community during the 1960s through the 1980s, is now experiencing housing deterioration, economic disinvestment, and increased social needs. ^ Although the City developed a Community Development Plan for the neighborhood addressing the neighborhood problems, needs, and objectives, it failed to address and take advantage of the area's prominent commercial street, Calle Ocho, as a cultural catalyst for the revitalization of the neighborhood. With an urban study and understanding of the area's needs for transit system improvements, program analysis, and a valuable architectural inventory, an intervention project can be developed. The project will capitalize on the area's historical and cultural assets and serve as a step towards altering the area's decline and revitalizing the street and community to recapture the energy present during the early years of the massive Cuban migration. ^

Análisis de preferencias del paisaje urbano entre barrios compactos y barrios postindustriales en Vitoria-Gasteiz. Implicaciones en la planificación urbana

Las características urbanísticas de las expansiones urbanas postindustriales desarrolladas en las últimas décadas en numerosas ciudades españolas presentan diferencias notables con las de barrios centrales y pericentrales más compactos preexistentes. Con el fin de estudiar cómo son percibidas por los ciudadanos de Vitoria-Gasteiz dichas diferencias urbanísticas, se realizaron 250 encuestas a residentes en los barrios compactos de la ciudad sobre sus preferencias entre el paisaje urbano de su barrio y el de los barrios postindustriales. Se observó que la gran mayoría de los encuestados prefirieron su compacto barrio en aspectos de sociabilidad, accesibilidad a servicios y bienestar global. Los resultados obtenidos se contrastaron con los de un estudio previo en el que una encuesta similar fue realizada a residentes en un barrio postindustrial. Se discuten las implicaciones de los resultados para desarrollar una práctica urbanística más sostenible y que integre la percepción de los usuarios de la ciudad.

Circuit Quantum Electrodynamics with Transmon Qubits in the Ultrastrong Coupling Regime

68 pg.

Practical, appropriate, empirically-validated guidelines for designing educational games

There has recently been a great deal of interest in the potential of computer games to function as innovative educational tools. However, there is very little evidence of games fulfilling that potential. Indeed, the process of merging the disparate goals of education and games design appears problematic, and there are currently no practical guidelines for how to do so in a coherent manner. In this paper, we describe the successful, empirically validated teaching methods developed by behavioural psychologists and point out how they are uniquely suited to take advantage of the benefits that games offer to education. We conclude by proposing some practical steps for designing educational games, based on the techniques of Applied Behaviour Analysis. It is intended that this paper can both focus educational games designers on the features of games that are genuinely useful for education, and also introduce a successful form of teaching that this audience may not yet be familiar with.

Blackcloud

The work was derived from terrestrial laser scan data of a bio-diverse landscape on the SE coast of Western Australia. The digital three dimensional scan data has been converged and then a portion of that computer aided design (CAD) file has been captured via ‘screen capture’ to produce Blackcloud.---------- The primary intention behind the production of the work was to expand understanding on the means of representing and then designing for sites in ‘kwongan’ landscapes which are constituted by highly biodiverse, bushfire prone heath vegetation.

Before and after the fire

The work was derived from terrestrial laser scan data of a bio-diverse landscape on the SE coast of Western Australia. The scanning was conducted both before and after a significant bushfire event. The digital three dimensional scan data has been converged and then abstracted into a two dimensional vertical sections or slice which reveals the vegetal surface of heath vegetation and the surface of the landform.---------- This abstraction converts the complex data into spatial information so that it is meaningful in the context the architectural and landscape architectural design process. The primary intention behind the production of the work was to expand understanding on the means of representing and then designing for sites in ‘kwongan’ landscapes which are constituted by highly biodiverse, bushfire prone heath vegetation.

Heathprint

The work was derived from terrestrial laser scan data of a bio-diverse landscape on the SE coast of Western Australia. The digital three dimensional scan data has been abstracted into two dimensional horizontal sections or slices. This abstraction converts the complex data into spatial information which is meaningful in the context of the act of architectural and landscape architectural design. The primary intention behind the production of the work was to expand understanding on the means of representing and then designing for sites in 'kwongan' landscapes which are constituted by highly biodiverse - and thus difficult to measure - heath vegetation. From Heathprint the author generated contour intervals of the landform upon which an associate (Daniela Simon architect) designed a work of architecture, which subsequently was awarded a commendation for residential architecture in the WA Chapter Australia Institute of Architects awards 2007.

Neighborhood disadvantage and physical activity : baseline results from the HABITAT multilevel longitudinal study

PURPOSE: To examine the association between neighborhood disadvantage and physical activity (PA). ---------- METHODS: We use data from the HABITAT multilevel longitudinal study of PA among mid-aged (40-65 years) men and women (n=11, 037, 68.5% response rate) living in 200 neighborhoods in Brisbane, Australia. PA was measured using three questions from the Active Australia Survey (general walking, moderate, and vigorous activity), one indicator of total activity, and two questions about walking and cycling for transport. The PA measures were operationalized using multiple categories based on time and estimated energy expenditure that were interpretable with reference to the latest PA recommendations. The association between neighborhood disadvantage and PA was examined using multilevel multinomial logistic regression and Markov Chain Monte Carlo simulation. The contribution of neighborhood disadvantage to between-neighborhood variation in PA was assessed using the 80% interval odds ratio. ---------- RESULTS: After adjustment for sex, age, living arrangement, education, occupation, and household income, reported participation in all measures and levels of PA varied significantly across Brisbane’s neighborhoods, and neighborhood disadvantage accounted for some of this variation. Residents of advantaged neighborhoods reported significantly higher levels of total activity, general walking, moderate, and vigorous activity; however, they were less likely to walk for transport. There was no statistically significant association between neighborhood disadvantage and cycling for transport. In terms of total PA, residents of advantaged neighborhoods were more likely to exceed PA recommendations. ---------- CONCLUSIONS: Neighborhoods may exert a contextual effect on residents’ likelihood of participating in PA. The greater propensity of residents in advantaged neighborhoods to do high levels of total PA may contribute to lower rates of cardiovascular disease and obesity in these areas

Neighbourhood disadvantage, individual-level socioeconomic position, and self-reported chronic arthritis : a cross-sectional multilevel study

Objective: To examine the association between individual- and neighborhood-level disadvantage and self-reported arthritis. Methods: We used data from a population-based cross-sectional study conducted in 2007 among 10,757 men and women ages 40–65 years, selected from 200 neighborhoods in Brisbane, Queensland, Australia using a stratified 2-stage cluster design. Data were collected using a mail survey (68.5% response). Neighborhood disadvantage was measured using a census-based composite index, and individual disadvantage was measured using self-reported education, household income, and occupation. Arthritis was indicated by self-report. Data were analyzed using multilevel modeling. Results: The overall rate of self-reported arthritis was 23% (95% confidence interval [95% CI] 22–24). After adjustment for sociodemographic factors, arthritis prevalence was greatest for women (odds ratio [OR] 1.5, 95% CI 1.4–1.7) and in those ages 60–65 years (OR 4.4, 95% CI 3.7–5.2), those with a diploma/associate diploma (OR 1.3, 95% CI 1.1–1.6), those who were permanently unable to work (OR 4.0, 95% CI 3.1–5.3), and those with a household income <$25,999 (OR 2.1, 95% CI 1.7–2.6). Independent of individual-level factors, residents of the most disadvantaged neighborhoods were 42% (OR 1.4, 95% CI 1.2–1.7) more likely than those in the least disadvantaged neighborhoods to self-report arthritis. Cross-level interactions between neighborhood disadvantage and education, occupation, and household income were not significant. Conclusion: Arthritis prevalence is greater in more socially disadvantaged neighborhoods. These are the first multilevel data to examine the relationship between individual- and neighborhood-level disadvantage upon arthritis and have important implications for policy, health promotion, and other intervention strategies designed to reduce the rates of arthritis, indicating that intervention efforts may need to focus on both people and places.

Augmenting analytical CRM strategies with social BI

Large communities built around social media on the Internet offer an opportunity to augment analytical customer relationship management (CRM) strategies. The purpose of this paper is to provide direction to advance the conceptual design of business intelligence (BI) systems for implementing CRM strategies. After introducing social CRM and social BI as emerging fields of research, the authors match CRM strategies with a re-engineered conceptual data model of Facebook in order to illustrate the strategic value of these data. Subsequently, the authors design a multi-dimensional data model for social BI and demonstrate its applicability by designing management reports in a retail scenario. Building on the service blueprinting framework, the authors propose a structured research agenda for the emerging field of social BI.