Protein and Drug Design Algorithms Using Improved Biophysical Modeling

This thesis focuses on the development of algorithms that will allow protein design calculations to incorporate more realistic modeling assumptions. Protein design algorithms search large sequence spaces for protein sequences that are biologically and medically useful. Better modeling could improve the chance of success in designs and expand the range of problems to which these algorithms are applied. I have developed algorithms to improve modeling of backbone flexibility (DEEPer) and of more extensive continuous flexibility in general (EPIC and LUTE). I’ve also developed algorithms to perform multistate designs, which account for effects like specificity, with provable guarantees of accuracy (COMETS), and to accommodate a wider range of energy functions in design (EPIC and LUTE).

Education - research - practice

Through this paper we will look at links between architecture education, research and practice, using a current project as a vehicle to cover aspects of building, pilot and live project. The first aspect, the building project consists of the refurbishment and extension of a Parnell Cottage for a private client and is located near Cloyne, in East Cork, Ireland. The pilot project falls within the NEES Project, investigating the use of materials and services based on natural or recycled materials to improve the energy performance of new and existing buildings. The live project aims to hold a series of on site workshops and seminars for students of Architecture, Architects and interested parties, demonstrating the integration of the NEES best practice materials and techniques within the built project. The workshops, seminars and key project documents will be digitally recorded for dissemination through a web based publication. The small scale of the building project allowed for flexibility in the early conceptual design stages and the integration of the research and educational aspects.

Using parent report to assess early lexical production in children exposed to more than one language

Limited expressive vocabulary skills in young children are considered to be the first warning signs of a potential Specific Language Impairment (SLI) (Ellis & Thal, 2008). In bilingual language learning environments, the expressive vocabulary size in each of the child’s developing languages is usually smaller compared to the number of words produced by monolingual peers (e.g. De Houwer, 2009). Nonetheless, evidence shows children’s total productive lexicon size across both languages to be comparable to monolingual peers’ vocabularies (e.g. Pearson et al., 1993; Pearson & Fernandez, 1994). Since there is limited knowledge as to which level of bilingual vocabulary size should be considered as a risk factor for SLI, the effects of bilingualism and language-learning difficulties on early lexical production are often confounded. The compilation of profiles for early vocabulary production in children exposed to more than one language, and their comparison across language pairs, should enable more accurate identification of vocabulary delays that signal a risk for SLI in bilingual populations. These considerations prompted the design of a methodology for assessing early expressive vocabulary in children exposed to more than one language, which is described in the present chapter. The implementation of this methodological framework is then outlined by presenting the design of a study that measured the productive lexicons of children aged 24-36 months who were exposed to different language pairs, namely Maltese and English, Irish and English, Polish and English, French and Portuguese, Turkish and German as well as English and Hebrew. These studies were designed and coordinated in COST Action IS0804 Working Group 3 (WG3) and will be described in detail in a series of subsequent publications. Expressive vocabulary size was measured through parental report, by employing the vocabulary checklist of the MacArthur-Bates Communicative Development Inventory: Words and Sentences (CDI: WS) (Fenson et al., 1993, 2007) and its adaptations to the participants’ languages. Here we describe the novelty of the study’s methodological design, which lies in its attempt to harmonize the use of vocabulary checklist adaptations, together with parental questionnaires addressing language exposure and developmental history, across participant groups characterized by different language exposure variables. This chapter outlines the various methodological considerations that paved the way for meaningful cross-linguistic comparison of the participants’ expressive lexicon sizes. In so doing, it hopes to provide a template for and encourage further research directed at establishing a threshold for SLI risk in children exposed to more than one language.

Nurses' knowledge of advance directives and perceived confidence in end-of-life care: a cross-sectional study in five countries

Nurses' knowledge regarding advance directives may affect their administration and completion in end-of-life care. Confidence among nurses is a barrier to the provision of quality end-of-life care. This study investigated nurses' knowledge of advance directives and perceived confidence in end-of-life care, in Hong Kong, Ireland, Israel, Italy and the USA using a cross-sectional descriptive design (n = 1089). In all countries, older nurses and those who had more professional experience felt more confident managing patients' symptoms at end-of-life and more comfortable stopping preventive medications at end-of-life. Nurses in the USA reported that they have more knowledge and experience of advance directives compared with other countries. In addition, they reported the highest levels of confidence and comfort in dealing with end-of-life care. Although legislation for advance directives does not yet exist in Ireland, nurses reported high levels of confidence in end-of-life care.

Learning Environments in Design Studio Culture

The paper reports on a study of design studio culture from a student perspective. Learning in design studio culture has been theorised variously as a signature pedagogy emulating professional practice models, as a community of practice and as a form of problem-based learning, all largely based on the study of teaching events in studio. The focus of this research has extended beyond formally recognized activities to encompass the student’s experience of their social and community networks, working places and study set-ups, to examine how these have contributed to studio culture and how there have been supported by studio teaching. Semi-structured interviews with final year undergraduate students of architecture formed the basis of the study using an interpretivist approach informed by Actor-network theory, with studio culture featured as the focal actor, enrolling students and engaging with other actors, together constituting an actor-network of studio culture. The other actors included social community patterns and activities; the numerous working spaces (including but not limited to the studio space itself); the equipment, tools of trade and material pre-requisites for working; the portfolio enrolling the other actors to produce work for it; and the various formal and informal events associated with the course itself. Studio culture is a highly charged social arena: The question is how, and in particular, which aspects of it support learning? Theoretical models of situated learning and communities of practice models have informed the analysis, with Bourdieu’s theory of practice, and his interrelated concepts of habitus, field and capital providing a means of relating individually acquired habits and modes of working to social contexts. Bourdieu’s model of habitus involves the externalisation through the social realm of habits and knowledge previously internalised. It is therefore a useful model for considering whole individual learning activities; shared repertoires and practices located in the social realm. The social milieu of the studio provides a scene for the exercise and display of ‘practicing’ and the accumulation of a form of ‘practicing-capital’. This capital is a property of the social milieu rather than the space, so working or practicing in the company of others (in space and through social media) becomes a more valued aspect of studio than space or facilities alone. This practicing-capital involves the acquisition of a habitus of studio culture, with the transformation of physical practices or habits into social dispositions, acquiring social capital (driving the social milieu) and cultural capital (practicing-knowledge) in the process. The research drew on students’ experiences, and their practicing ‘getting a feel for the game’ by exploring the limits or boundaries of the field of studio culture. The research demonstrated that a notional studio community was in effect a social context for supporting learning; a range of settings to explore and test out newly internalised knowledge, demonstrate or display ideas, modes of thinking and practicing. The study presents a nuanced interpretation of how students relate to a studio culture that involves a notional community, and a developing habitus within a field of practicing that extends beyond teaching scenarios.

Who is in charge? An L2 Discourse Intonation Study on Four Prosodic Parameters to Exert the Pragmatic Function of Dominance and Control in the Context of L2 Non-specialist Public Speaking

This paper reports the findings from a study of the learning of English intonation by Spanish speakers within the discourse mode of L2 oral presentation. The purpose of this experiment is, firstly, to compare four prosodic parameters before and after an L2 discourse intonation training programme and, secondly, to confirm whether subjects, after the aforementioned L2 discourse intonation training, are able to match the form of these four prosodic parameters to the discourse-pragmatic function of dominance and control. The study designed the instructions and tasks to create the oral and written corpora and Brazil’s Pronunciation for Advanced Learners of English was adapted for the pedagogical aims of the present study. The learners’ pre- and post-tasks were acoustically analysed and a pre / post- questionnaire design was applied to interpret the acoustic analysis. Results indicate most of the subjects acquired a wider choice of the four prosodic parameters partly due to the prosodically-annotated transcripts that were developed throughout the L2 discourse intonation course. Conversely, qualitative and quantitative data reveal most subjects failed to match the forms to their appropriate pragmatic functions to express dominance and control in an L2 oral presentation.

Hur grafiska formgivare runt om i världen uppfattar skandinavisk grafisk design

Syftet med föreliggande studie har varit att kartlägga hur grafiska formgivare runt om i världen uppfattar skandinavisk grafisk design. 53 deltagare från industriländer deltog i studien som använde en kombination av mail-intervjuer och enkäter. Resultaten från denna studie indikerar att, oavsett kontinent, upplevs skandinavisk grafisk design som enkel och funktionell. Layouten uppfattades som rutnätsbaserad med mycket ljusrum och få grafiska element. Monokroma färger som svart, vit och grå utan gradienter och skuggor uppfattades som typiska för skandinavisk grafisk design; följt av jord- och pastellfärger. Sanserifer var mest förknippade med skandinavisk grafisk design. Motiv ansågs i denna studie att användas sparsamt, men när de används avbildar de naturen eller geometriska former. Foton och illustrationer ansågs användas ungefär lika mycket, illustrationer hade en smärre större preferens. Den upplevda påverkan av skandinavisk grafisk design varierade mellan deltagarna. Deltagarna som tyckte att påverkan var stor, ansåg att detta berodde på förespråkandet av enkelhet och funktion, sammanflätning av designområden och/eller frammaning av hållbar grafisk design. Deltagarna som ansåg att påverkan var låg, tyckte att för lite publicitet var en bidragande faktor.De flesta deltagarna i denna undersökning ansåg att skandinavisk grafisk design var enklare i jämförelse med vad de kunde se i sina hemländer. Vidare tyckte afrikanska, asiatiska och sydamerikanska deltagare  att färgerna hade lägre kroma.

Étude d’évaluabilité et évaluation des processus et des effets d’un programme de prévention de l’usage de substances psychoactives lors de la transition primaire-secondaire

La mise en œuvre d’activités de prévention de la consommation de substances psychoactives (SPA) (tabac, alcool et cannabis) en milieu scolaire est une stratégie couramment utilisée pour rejoindre un grand nombre de jeunes. Ces activités s’inspirent, soit de programmes existant, soit d’innovations dictées par le contexte d’implantation ou l’existence de données de recherche. Dans un cas comme dans l’autre, l’évaluation de ces programmes représente la meilleure voie pour mesurer leur efficacité et/ou connaître comment ceux-ci sont implantés. C’est cet impératif qui a motivé une commission scolaire du Québec a recommandé l’évaluation de l’Intervention en Réseau (IR), un programme développé en vue de retarder l’âge d’initiation et de réduire la consommation problématique de SPA chez les élèves. Ce programme adopte une approche novatrice avec pour principal animateur un intervenant pivot (IP) qui assure le suivi des élèves de la 5e année du primaire jusqu’en 3e secondaire. Inspiré des modèles en prévention de la santé et de l’Approche École en santé (AES), le rôle de l’IP ici se démarque de ceux-ci. Certes, il est l’interface entre les différents acteurs impliqués et les élèves mais dans le cadre du programme IR, l’IP est intégré dans les écoles primaires et secondaires qu’il dessert. C’est cet intervenant qui assure la mobilisation des autres acteurs pour la mise en œuvre des activités. Cette thèse vise à rendre compte de ce processus d’évaluation ainsi que des résultats obtenus. L’approche d’évaluation en est une de type participatif et collaboratif avec des données quantitatives et qualitatives recueillies par le biais de questionnaires, d’entrevues, de groupes de discussion, d’un journal de bord et de notes de réunions. Les données ont été analysées dans le cadre de trois articles dont le premier concerne l’étude d’évaluabilité (ÉÉ) du programme. Les participants de cette ÉÉ sont des acteurs-clés du programme (N=13) rencontrés en entrevues. Une analyse documentaire (rapports et journal de bord) a également été effectuée. Cette ÉÉ a permis de clarifier les intentions des initiateurs du programme et les objectifs poursuivis par ces derniers. Elle a également permis de rendre la théorie du programme plus explicite et de développer le modèle logique, deux éléments qui ont facilité les opérations d’évaluation qui ont suivi. Le deuxième article porte sur l’évaluation des processus en utilisant la théorie de l’acteur-réseau (TAR) à travers ses quatre moments du processus de traduction des innovations (la problématisation, l’intéressement, l’enrôlement et la mobilisation des alliés), l’analyse des controverses et du rôle des acteurs humains et non-humains. Après l’analyse des données obtenues par entrevues auprès de 19 informateurs-clés, les résultats montrent que les phases d’implantation du programme passent effectivement par les quatre moments de la TAR, que la gestion des controverses par la négociation et le soutien était nécessaire pour la mobilisation de certains acteurs humains. Cette évaluation des processus a également permis de mettre en évidence le rôle des acteurs non-humains dans le processus d’implantation du programme. Le dernier article concerne une évaluation combinée des effets (volet quantitatif) et des processus (volet qualitatif) du programme. Pour le volet quantitatif, un devis quasi-expérimental a été adopté et les données ont été colligées de façon longitudinale par questionnaires auprès de 901 élèves de 5e et 6e année du primaire et leurs enseignants de 2010 à 2014. L’analyse des données ont montré que le programme n’a pas eu d’effets sur l’accessibilité et les risques perçus, l’usage problématique d’alcool et la polyconsommation (alcool et cannabis) chez les participants. Par contre, les résultats suggèrent que le programme pourrait favoriser la réduction du niveau de consommation et retarder l’âge d’initiation à l’alcool et au cannabis. Ils suggèrent également un effet potentiellement positif du programme sur l’intoxication à l’alcool chez les élèves. Quant au volet qualitatif, il a été réalisé à l’aide d’entrevues avec les intervenants (N=17), de groupes de discussion avec des élèves du secondaire (N=10) et d’une analyse documentaire. Les résultats montrent que le programme bénéficie d’un préjugé favorable de la part des différents acteurs ayant participé à l’évaluation et est bien acceptée par ces derniers. Cependant, le roulement fréquent de personnel et le grand nombre d’écoles à suivre peuvent constituer des obstacles à la bonne marche du programme. En revanche, le leadership et le soutien des directions d’écoles, la collaboration des enseignants, les qualités de l’IP et la flexibilité de la mise en œuvre sont identifiés comme des éléments ayant contribué au succès du programme. Les résultats et leur implication pour les programmes et l’évaluation sont discutés. Enfin, un plan de transfert des connaissances issues de la recherche évaluative est proposé.

Making the user more efficient: Design for sustainable behaviour

User behaviour is a significant determinant of a product’s environmental impact; while engineering advances permit increased efficiency of product operation, the user’s decisions and habits ultimately have a major effect on the energy or other resources used by the product. There is thus a need to change users’ behaviour. A range of design techniques developed in diverse contexts suggest opportunities for engineers, designers and other stakeholders working in the field of sustainable innovation to affect users’ behaviour at the point of interaction with the product or system, in effect ‘making the user more efficient’. Approaches to changing users’ behaviour from a number of fields are reviewed and discussed, including: strategic design of affordances and behaviour-shaping constraints to control or affect energyor other resource-using interactions; the use of different kinds of feedback and persuasive technology techniques to encourage or guide users to reduce their environmental impact; and context-based systems which use feedback to adjust their behaviour to run at optimum efficiency and reduce the opportunity for user-affected inefficiency. Example implementations in the sustainable engineering and ecodesign field are suggested and discussed.

It's Not Rocket Library Science: Design Epistemology and American Librarianship

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

Drawing in Duos: The Journeys and Intersections Collaboration Project Between Istanbul and Worcester

This paper focuses on a collaborative drawing project carried out between two undergraduate drawing courses, one in İstanbul and the other in Worcester, during the Fall 2015 semester. Duos -teams of two working remotely- took turns to work on the same drawing in correspondence for three months by means of communication and sharing the changing images on-line with one another. The project introduced a collaborative method of learning based on drawing, initiated cultural exchange and cooperation. The role of drawing in the project was critical due to the direct but gradual nature of transmitting meaning onto paper. Outcomes of this project consisted of a flexible and playful creation process for students making use of the element of chance. They sought alternate ways to finalize a drawing and experienced the benefits of artistic co-production. The project has the capacity to inspire artists, instructors and others interested in creative partnership in different disciplines and can be of value as an educational model.

Radio over fiber enabling PON fronthaul in a two-tiered cloud

Avec l’avènement des objets connectés, la bande passante nécessaire dépasse la capacité des interconnections électriques et interface sans fils dans les réseaux d’accès mais aussi dans les réseaux coeurs. Des systèmes photoniques haute capacité situés dans les réseaux d’accès utilisant la technologie radio sur fibre systèmes ont été proposés comme solution dans les réseaux sans fil de 5e générations. Afin de maximiser l’utilisation des ressources des serveurs et des ressources réseau, le cloud computing et des services de stockage sont en cours de déploiement. De cette manière, les ressources centralisées pourraient être diffusées de façon dynamique comme l’utilisateur final le souhaite. Chaque échange nécessitant une synchronisation entre le serveur et son infrastructure, une couche physique optique permet au cloud de supporter la virtualisation des réseaux et de les définir de façon logicielle. Les amplificateurs à semi-conducteurs réflectifs (RSOA) sont une technologie clé au niveau des ONU(unité de communications optiques) dans les réseaux d’accès passif (PON) à fibres. Nous examinons ici la possibilité d’utiliser un RSOA et la technologie radio sur fibre pour transporter des signaux sans fil ainsi qu’un signal numérique sur un PON. La radio sur fibres peut être facilement réalisée grâce à l’insensibilité a la longueur d’onde du RSOA. Le choix de la longueur d’onde pour la couche physique est cependant choisi dans les couches 2/3 du modèle OSI. Les interactions entre la couche physique et la commutation de réseaux peuvent être faites par l’ajout d’un contrôleur SDN pour inclure des gestionnaires de couches optiques. La virtualisation réseau pourrait ainsi bénéficier d’une couche optique flexible grâce des ressources réseau dynamique et adaptée. Dans ce mémoire, nous étudions un système disposant d’une couche physique optique basé sur un RSOA. Celle-ci nous permet de façon simultanée un envoi de signaux sans fil et le transport de signaux numérique au format modulation tout ou rien (OOK) dans un système WDM(multiplexage en longueur d’onde)-PON. Le RSOA a été caractérisé pour montrer sa capacité à gérer une plage dynamique élevée du signal sans fil analogique. Ensuite, les signaux RF et IF du système de fibres sont comparés avec ses avantages et ses inconvénients. Finalement, nous réalisons de façon expérimentale une liaison point à point WDM utilisant la transmission en duplex intégral d’un signal wifi analogique ainsi qu’un signal descendant au format OOK. En introduisant deux mélangeurs RF dans la liaison montante, nous avons résolu le problème d’incompatibilité avec le système sans fil basé sur le TDD (multiplexage en temps duplexé).

In-house Preparation of Examination Papers using troff, tbl, and eqn.

Starting in December 1982 the University of Nottingham decided to phototypeset almost all of its examination papers `in house' using the troff, tbl and eqn programs running under UNIX. This tutorial lecture highlights the features of the three programs with particular reference to their strengths and weaknesses in a production environment. The following issues are particularly addressed: Standards -- all three software packages require the embedding of commands and the invocation of pre-written macros, rather than `what you see is what you get'. This can help to enforce standards, in the absence of traditional compositor skills. Hardware and Software -- the requirements are analysed for an inexpensive preview facility and a low-level interface to the phototypesetter. Mathematical and Technical papers -- the fine-tuning of eqn to impose a standard house style. Staff skills and training -- systems of this kind do not require the operators to have had previous experience of phototypesetting. Of much greater importance is willingness and flexibility in learning how to use computer systems.

Design of unique composites based on aromatic thermosetting copolyesters

Aromatic thermosetting copolyester (ATSP) has promise in high-temperature applications. It can be employed as a bulk polymer, as a coating and as a matrix for carbon fiber composites (ATSP/C composites). This work focuses on the applications of high performance ATSP/C composites. The morphology of the ATSP matrix in the presence of carbon fiber was studied. The effect of liquid crystalline character of starting oligomers used to prepare ATSP on the final crystal structure of the ATSP/C composite was evaluated. Matrices obtained by crosslinking of both liquid crystalline oligomers (ATSP2) and non-liquid crystalline oligomers (ATSP1) tend to crystallize in presence of carbon fibers. The crystallite size of ATSP2 is 4 times that of ATSP1. Composites made from ATSP2 yield tougher matrices compared to those made from ATSP1. Thus toughened matrices could be achieved without incorporating any additives by just changing the morphology of the final polymer. The flammability characteristics of ATSP were also studied. The limiting oxygen index (LOI) of bulk ATSP was found to be 40% whereas that of ATSP/C composites is estimated to be 85%. Thus, ATSP shows potential to be used as a flame resistant material, and also as an aerospace reentry shield. Mechanical properties of the ATSP/C composite were characterized. ATSP was observed to bond strongly with reinforcing carbon fibers. The tensile strength, modulus and shear modulus were comparable to those of conventionally used high temperature epoxy resins. ATSP shows a unique capability for healing of interlaminar cracks on application of heat and pressure, via the Interchain Transesterification Reaction (ITR). ITR can also be used for reduction in void volume and healing of microcracks. Thus, ATSP resin systems provide a unique intrinsic repair mechanism compared to any other thermosetting systems in use today. Preliminary studies on measurement of residual stresses for ATSP/C composites indicate that the stresses induced are much lower than that in epoxy/C composites. Thermal fatigue testing suggests that ATSP shows better resistance to microcracking compared to epoxy resins.

The Effect of using online homework exercises on student achievement in a Quantitative methods course

Abstract: Quantitative Methods (QM) is a compulsory course in the Social Science program in CEGEP. Many QM instructors assign a number of homework exercises to give students the opportunity to practice the statistical methods, which enhances their learning. However, traditional written exercises have two significant disadvantages. The first is that the feedback process is often very slow. The second disadvantage is that written exercises can generate a large amount of correcting for the instructor. WeBWorK is an open-source system that allows instructors to write exercises which students answer online. Although originally designed to write exercises for math and science students, WeBWorK programming allows for the creation of a variety of questions which can be used in the Quantitative Methods course. Because many statistical exercises generate objective and quantitative answers, the system is able to instantly assess students’ responses and tell them whether they are right or wrong. This immediate feedback has been shown to be theoretically conducive to positive learning outcomes. In addition, the system can be set up to allow students to re-try the problem if they got it wrong. This has benefits both in terms of student motivation and reinforcing learning. Through the use of a quasi-experiment, this research project measured and analysed the effects of using WeBWorK exercises in the Quantitative Methods course at Vanier College. Three specific research questions were addressed. First, we looked at whether students who did the WeBWorK exercises got better grades than students who did written exercises. Second, we looked at whether students who completed more of the WeBWorK exercises got better grades than students who completed fewer of the WeBWorK exercises. Finally, we used a self-report survey to find out what students’ perceptions and opinions were of the WeBWorK and the written exercises. For the first research question, a crossover design was used in order to compare whether the group that did WeBWorK problems during one unit would score significantly higher on that unit test than the other group that did the written problems. We found no significant difference in grades between students who did the WeBWorK exercises and students who did the written exercises. The second research question looked at whether students who completed more of the WeBWorK exercises would get significantly higher grades than students who completed fewer of the WeBWorK exercises. The straight-line relationship between number of WeBWorK exercises completed and grades was positive in both groups. However, the correlation coefficients for these two variables showed no real pattern. Our third research question was investigated by using a survey to elicit students’ perceptions and opinions regarding the WeBWorK and written exercises. Students reported no difference in the amount of effort put into completing each type of exercise. Students were also asked to rate each type of exercise along six dimensions and a composite score was calculated. Overall, students gave a significantly higher score to the written exercises, and reported that they found the written exercises were better for understanding the basic statistical concepts and for learning the basic statistical methods. However, when presented with the choice of having only written or only WeBWorK exercises, slightly more students preferred or strongly preferred having only WeBWorK exercises. The results of this research suggest that the advantages of using WeBWorK to teach Quantitative Methods are variable. The WeBWorK system offers immediate feedback, which often seems to motivate students to try again if they do not have the correct answer. However, this does not necessarily translate into better performance on the written tests and on the final exam. What has been learned is that the WeBWorK system can be used by interested instructors to enhance student learning in the Quantitative Methods course. Further research may examine more specifically how this system can be used more effectively.