Modelling and Mining To Manage

In this talk, I will describe various computational modelling and data mining solutions that form the basis of how the office of Deputy Head of Department (Resources) works to serve you. These include lessons I learn about, and from, optimisation issues in resource allocation, uncertainty analysis on league tables, modelling the process of winning external grants, and lessons we learn from student satisfaction surveys, some of which I have attempted to inject into our planning processes.

Exploration génétique de l'hypothyroïdie congénitale par dysgénésie thyroïdienne

L'hypothyroïdie congénitale par dysgénésie thyroïdienne (HCDT, ectopie dans plus de 80 %) a une prévalence de 1 cas sur 4000 naissances vivantes. L’HCDT est la conséquence d'une défaillance de la thyroïde embryonnaire à se différencier, à se maintenir ou à migrer vers sa localisation anatomique (partie antérieure du cou), qui aboutit à une absence totale de la thyroïde (athyréose) ou à une ectopie thyroïdienne (linguale ou sublinguale). Les HCDT sont principalement non-syndromiques (soit 98% des cas sont non-familiale), ont un taux de discordance de 92% chez les jumeaux monozygotes, et ont une prédominance féminine et ethnique (i.e., Caucasienne). La majorité des cas d’HCDT n’a pas de cause connue, mais est associée à un déficit sévère en hormones thyroïdiennes (hypothyroïdie). Des mutations germinales dans les facteurs de transcription liés à la thyroïde (NKX2.1, FOXE1, PAX8, NKX2.5) ont été identifiées dans seulement 3% des patients atteints d’HCDT sporadiques et l’analyse de liaisons exclue ces gènes dans les rares familles multiplex avec HCDT. Nous supposons que le manque de transmission familiale claire d’HCDT peut résulter de la nécessité d’au moins deux « hits » génétiques différents dans des gènes importants pour le développement thyroïdien. Pour répondre au mieux nos questions de recherche, nous avons utilisé deux approches différentes: 1) une approche gène candidat, FOXE1, seul gène impliqué dans l’ectopie dans le modèle murin et 2) une approche en utilisant les techniques de séquençage de nouvelle génération (NGS) afin de trouver des variants génétiques pouvant expliquer cette pathologie au sein d’une cohorte de patients avec HCDT. Pour la première approche, une étude cas-contrôles a été réalisée sur le promoteur de FOXE1. Il a récemment été découvert qu’une région du promoteur de FOXE1 est différentiellement méthylée au niveau de deux dinucléotides CpG consécutifs, définissant une zone cruciale de contrôle de l’expression de FOXE1. L’analyse d’association basée sur les haplotypes a révélé qu’un haplotype (Hap1: ACCCCCCdel1C) est associé avec le HCDT chez les Caucasiens (p = 5x10-03). Une réduction significative de l’activité luciférase est observée pour Hap1 (réduction de 68%, p<0.001) comparé au promoteur WT de FOXE1. Une réduction de 50% de l’expression de FOXE1 dans une lignée de cellules thyroïdienne humaine est suffisante pour réduire significativement la migration cellulaire (réduction de 55%, p<0.05). Un autre haplotype (Hap2: ACCCCCCC) est observé moins fréquemment chez les Afro-Américain comparés aux Caucasiens (p = 1.7x10-03) et Hap2 diminue l’activité luciférase (réduction de 26%, p<0.001). Deux haplotypes distincts sont trouvés fréquemment dans les contrôles Africains (Black-African descents). Le premier haplotype (Hap3: GTCCCAAC) est fréquent (30.2%) chez les contrôles Afro-Américains comparés aux contrôles Caucasiens (6.3%; p = 2.59 x 10-9) tandis que le second haplotype (Hap4: GTCCGCAC) est trouvé exclusivement chez les contrôles Afro-Américains (9.4%) et est absent chez les contrôles Caucasiens (P = 2.59 x 10-6). Pour la deuxième approche, le séquençage de l’exome de l’ADN leucocytaire entre les jumeaux MZ discordants n’a révélé aucune différence. D'où l'intérêt du projet de séquençage de l’ADN et l’ARN de thyroïdes ectopiques et orthotopiques dans lesquelles de l'expression monoallélique aléatoire dans a été observée, ce qui pourrait expliquer comment une mutation monoallélique peut avoir des conséquences pathogéniques. Finalement, le séquençage de l’exome d’une cohorte de 36 cas atteints d’HCDT a permis d’identifier de nouveaux variants probablement pathogéniques dans les gènes récurrents RYR3, SSPO, IKBKE et TNXB. Ces quatre gènes sont impliqués dans l’adhésion focale (jouant un rôle dans la migration cellulaire), suggérant un rôle direct dans les défauts de migration de la thyroïde. Les essais de migration montrent une forte diminution (au moins 60% à 5h) de la migration des cellules thyroïdiennes infectées par shRNA comparés au shCtrl dans 2 de ces gènes. Des zebrafish KO (-/- et +/-) pour ces nouveaux gènes seront réalisés afin d’évaluer leur impact sur l’embryologie de la thyroïde.

Moments of Rupture: Narratological Readings of Contemporary German Literature

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

A coupled movement and bioenergetics model to explore the spawning migration of anchovy in the Bay of Biscay

Adult anchovies in the Bay of Biscay perform north to south migration from late winter to early summer for spawning. However, what triggers and drives the geographic shift of the population remains unclear and poorly understood. An individual-based fish model has been implemented to explore the potential mechanisms that control anchovy's movement routes toward its spawning habitats. To achieve this goal, two fish movement behaviors – gradient detection through restricted area search and kinesis – simulated fish response to its dynamic environment. A bioenergetics model was used to represent individual growth and reproduction along the fish trajectory. The environmental forcing (food, temperature) of the model was provided by a coupled physical–biogeochemical model. We followed a hypothesis-testing strategy to actualize a series of simulations using different cues and computational assumptions. The gradient detection behavior was found as the most suitable mechanism to recreate the observed shift of anchovy distribution under the combined effect of sea-surface temperature and zooplankton. In addition, our results suggested that southward movement occurred more actively from early April to middle May following favorably the spatio-temporal evolution of zooplankton and temperature. In terms of fish bioenergetics, individuals who ended up in the southern part of the bay presented better condition based on energy content, proposing the resulting energy gain as an ecological explanation for this migration. The kinesis approach resulted in a moderate performance, producing distribution pattern with the highest spread. Finally, model performance was not significantly affected by changes on the starting date, initial fish distribution and number of particles used in the simulations, whereas it was drastically influenced by the adopted cues.

Too Much to Belong: Latina/o Racialization, Obesity Epidemic Discourse, and Unassimilable Corporeal Excess

This project examines the discursive constructions of Latina/o bodies as excessive in order to examine how Latinas/os are excluded from belonging to the U.S. nation-state. By approaching Latina/o Studies from a Fat Studies perspective, it works to more adequately address the role of embodiment in determining processes of racialization that directly impact Latinas/os in the United States, especially in light of the role of race and racism in “obesity epidemic” discourse. This dissertation argues that cultural and even physiological explanations about the Latina/o propensity for “overweight” and “obesity” create a discourse that marks the Latina/o body as demonstrating an unassimilable corporeal excess. In turn, the rhetoric of “diversity” and “multiculturalism” are rendered inapplicable to Latinas/os, as demonstrated by both nativist and seemingly pro-immigrant discourses that posit Latina/o physical excess in the form of fatness as detrimental and even dangerous to the U.S. nation-state.

Why is Asari (= Manila) clam Ruditapes philippinarum fitness poor in Arcachon Bay: a meta-analysis to answer?

Asari (= Manila) clam, Ruditapes philippinarum, is the second bivalve mollusc in terms of production in the world and, in many coastal areas, can beget important socio-economic issues. In Europe, this species was introduced after 1973. In Arcachon Bay, after a decade of aquaculture attempt, Asari clam rapidly constituted neo-naturalized population which is now fished. However, recent studies emphasized the decline of population and individual performances. In the framework of a national project (REPAMEP), some elements of fitness, stressors and responses in Arcachon bay were measured and compared to international data (41 publications, 9 countries). The condition index (CI=flesh weight/shell weight) was the lowest among all compared sites. Variation in average Chla concentration explained 30% of variation of CI among different areas. Among potential diseases, perkinsosis was particularly prevalent in Arcachon Bay, with high abundance, and Asari clams underwent Brown Muscle Disease, a pathology strictly restricted to this lagoon. Overall element contamination was relatively low, although arsenic, cobalt, nickel and chromium displayed higher values than in other ecosystems where Asari clam is exploited. Finally, total hemocyte count (THC) of Asari clam in Arcachon Bay, related to the immune system activity, exhibited values that were also under what is generally observed elsewhere. In conclusion, this study, with all reserves due to heterogeneity of available data, suggest that the particularly low fitness of Asari clam in Arcachon Bay is due to poor trophic condition, high prevalence and intensity of a disease (perkinsosis), moderate inorganic contamination, and poor efficiency of the immune system.

Percorrendo antigos [e recentes] trilhos do Megalitismo Alentejano

The archaeological excavation carried out in the last two decades by the author, as well as the study of data resulting from early works, allows us to understand that the megalithic monuments after being built have, in some cases, a long diachronic of reuses. Here is presented a brief summary of monuments, contexts and archaeological artefacts.

Stroke severity, early recovery and outcome are each related with clinical classification of stroke: data from the 'Tinzaparin in Acute Ischaemic Stroke Trial (TAIST)

Introduction: Baseline severity and clinical stroke syndrome (Oxford Community Stroke Project, OCSP) classification are predictors of outcome in stroke. We used data from the ‘Tinzaparin in Acute Ischaemic Stroke Trial’ (TAIST) to assess the relationship between stroke severity, early recovery, outcome and OCSP syndrome. Methods: TAIST was a randomised controlled trial assessing the safety and efficacy of tinzaparin versus aspirin in 1,484 patients with acute ischaemic stroke. Severity was measured as the Scandinavian Neurological Stroke Scale (SNSS) at baseline and days 4, 7 and 10, and baseline OCSP clinical classification recorded: total anterior circulation infarct (TACI), partial anterior circulation infarct (PACI), lacunar infarct (LACI) and posterior circulation infarction (POCI). Recovery was calculated as change in SNSS from baseline at day 4 and 10. The relationship between stroke syndrome and SNSS at days 4 and 10, and outcome (modified Rankin scale at 90 days) were assessed. Results: Stroke severity was significantly different between TACI (most severe) and LACI (mildest) at all four time points (p<0.001), with no difference between PACI and POCI. The largest change in SNSS score occurred between baseline and day 4; improvement was least in TACI (median 2 units), compared to other groups (median 3 units) (p<0.001). If SNSS did not improve by day 4, then early recovery and late functional outcome tended to be limited irrespective of clinical syndrome (SNSS, baseline: 31, day 10: 32; mRS, day 90: 4); patients who recovered early tended to continue to improve and had better functional outcome irrespective of syndrome (SNSS, baseline: 35, day 10: 50; mRS, day 90: 2). Conclusions: Although functional outcome is related to baseline clinical syndrome (best with LACI, worst with TACI), patients who improve early have a more favourable functional outcome, irrespective of their OCSP syndrome. Hence, patients with a TACI syndrome may still achieve a reasonable outcome if early recovery occurs.

Early allergen exposure and atopic eczema

Background The relationship between exposure to indoor aeroallergens in early life and subsequent eczema is unclear. We have previously failed to show any significant associations between early life exposure to house dust mite and cat fur allergens and either sensitization to these allergens or wheeze. We have also previously reported a lower prevalence of parent-reported, doctor-diagnosed eczema by age 2 years for children exposed to higher concentrations of house dust mite, but no other associations with other definitions of eczema or for exposure to cat allergen. Objectives To extend the exposure–response analysis of allergen exposure and eczema outcomes measured up to age 8 years, and to investigate the role of other genetic and environmental determinants. Methods A total of 593 children (92Æ4% of those eligible) born to all newly pregnant women attending one of three general practitioner surgeries in Ashford, Kent, were followed from birth to age 8 years. Concentrations of house dust mite and cat allergen were measured in dust samples collected from the home at 8 weeks after birth. The risk of subsequent eczema as defined by the U.K. diagnostic criteria was determined according to different levels (quintiles) of allergen exposure at birth. Results By age 8 years, 150 (25Æ3%) children had met the diagnostic criteria for eczema at least once. Visible flexural dermatitis was recorded at least once for 129 (28Æ0%). As in other studies, parental allergic history was positively associated with most eczema outcomes, as were higher maternal education and less crowded homes. No clear linear associations between early exposure to house dust mite or cat allergen were found, regardless of the definition of eczema used. The risk of eczema appeared to increase for the three lowest quintiles of house dust mite allergen exposure (odds ratio, OR 1Æ37 for third quintile compared with first), and then to fall for the two highest quintiles (OR 0Æ66 and 0Æ71) even after controlling for confounding factors. Conclusions The lack of any clear exposure–disease relationship between allergens in early life and subsequent eczema argues against allergen exposure being a major factor causing eczema. If the lower levels of eczema at higher levels of house dust mite are confirmed, then interventions aimed at reducing house dust mite in early infancy could paradoxically increase the risk of subsequent eczema.

BLACK SURVIVAL POLITICS: ORGANIZED MOBILIZATION STRATEGIES IN AFRICAN AMERICAN COMMUNITIES TO END THE HIV/AIDS EPIDEMIC

The purpose of this study is to examine organizational patterns of African American activism in response the HIV/AIDS epidemic. Given their political, economic, and social disenfranchisement, African Americans have historically developed protest and survival strategies to respond to the devaluation of their lives, health, and well-being. While Black protest strategies are typically regarded as oppositional and transformative, Black survival strategies have generally been conceptualized as accepting inequality. In the case of HIV/AIDS, African American religious and non-religious organizations were less likely to deploy protest strategies to ensure the survival and well-being of groups most at risk for HIV/AIDS—such as African American gay men and substance abusers. This study employs a multiple qualitative case study analysis of four African American organizations that were among the early mobilizers to respond to HIV/AIDS in Washington D.C. These organizations include two secular or community-based organizations and two Black churches or faith-based organizations. Given the association of HIV/AIDS with sexual sin and social deviance, I postulated that Black community-based organizations would be more responsive to the HIV/AIDS-related needs and interests of African Americans than their religious counterparts. More specifically, I expected that Black churches would be more conservative (i.e. maintain paternalistic heteronormative sexual standards) than the community-based organizations. Yet findings indicate that the Black churches in this study were more similar than different than the community-based organizations in their strategic responses to HIV/AIDS. Both the community-based organizations and Black churches drew upon three main strategies in ways that politicalize the struggle for Black survival—or what I regard as Black survival politics. First, Black survival strategies for HIV/AIDS include coalition building at the intersection of multiple systems of inequality, as well as on the levels of identity and community. Second, Black survival politics include altering aspects of religious norms and practices related to sex and sexuality. Third, Black survival politics relies on the resources of the government to provide HIV/AIDS related programs and initiatives that are, in large part, based on the gains made from collective action.

Exploration génétique de l'hypothyroïdie congénitale par dysgénésie thyroïdienne

L'hypothyroïdie congénitale par dysgénésie thyroïdienne (HCDT, ectopie dans plus de 80 %) a une prévalence de 1 cas sur 4000 naissances vivantes. L’HCDT est la conséquence d'une défaillance de la thyroïde embryonnaire à se différencier, à se maintenir ou à migrer vers sa localisation anatomique (partie antérieure du cou), qui aboutit à une absence totale de la thyroïde (athyréose) ou à une ectopie thyroïdienne (linguale ou sublinguale). Les HCDT sont principalement non-syndromiques (soit 98% des cas sont non-familiale), ont un taux de discordance de 92% chez les jumeaux monozygotes, et ont une prédominance féminine et ethnique (i.e., Caucasienne). La majorité des cas d’HCDT n’a pas de cause connue, mais est associée à un déficit sévère en hormones thyroïdiennes (hypothyroïdie). Des mutations germinales dans les facteurs de transcription liés à la thyroïde (NKX2.1, FOXE1, PAX8, NKX2.5) ont été identifiées dans seulement 3% des patients atteints d’HCDT sporadiques et l’analyse de liaisons exclue ces gènes dans les rares familles multiplex avec HCDT. Nous supposons que le manque de transmission familiale claire d’HCDT peut résulter de la nécessité d’au moins deux « hits » génétiques différents dans des gènes importants pour le développement thyroïdien. Pour répondre au mieux nos questions de recherche, nous avons utilisé deux approches différentes: 1) une approche gène candidat, FOXE1, seul gène impliqué dans l’ectopie dans le modèle murin et 2) une approche en utilisant les techniques de séquençage de nouvelle génération (NGS) afin de trouver des variants génétiques pouvant expliquer cette pathologie au sein d’une cohorte de patients avec HCDT. Pour la première approche, une étude cas-contrôles a été réalisée sur le promoteur de FOXE1. Il a récemment été découvert qu’une région du promoteur de FOXE1 est différentiellement méthylée au niveau de deux dinucléotides CpG consécutifs, définissant une zone cruciale de contrôle de l’expression de FOXE1. L’analyse d’association basée sur les haplotypes a révélé qu’un haplotype (Hap1: ACCCCCCdel1C) est associé avec le HCDT chez les Caucasiens (p = 5x10-03). Une réduction significative de l’activité luciférase est observée pour Hap1 (réduction de 68%, p<0.001) comparé au promoteur WT de FOXE1. Une réduction de 50% de l’expression de FOXE1 dans une lignée de cellules thyroïdienne humaine est suffisante pour réduire significativement la migration cellulaire (réduction de 55%, p<0.05). Un autre haplotype (Hap2: ACCCCCCC) est observé moins fréquemment chez les Afro-Américain comparés aux Caucasiens (p = 1.7x10-03) et Hap2 diminue l’activité luciférase (réduction de 26%, p<0.001). Deux haplotypes distincts sont trouvés fréquemment dans les contrôles Africains (Black-African descents). Le premier haplotype (Hap3: GTCCCAAC) est fréquent (30.2%) chez les contrôles Afro-Américains comparés aux contrôles Caucasiens (6.3%; p = 2.59 x 10-9) tandis que le second haplotype (Hap4: GTCCGCAC) est trouvé exclusivement chez les contrôles Afro-Américains (9.4%) et est absent chez les contrôles Caucasiens (P = 2.59 x 10-6). Pour la deuxième approche, le séquençage de l’exome de l’ADN leucocytaire entre les jumeaux MZ discordants n’a révélé aucune différence. D'où l'intérêt du projet de séquençage de l’ADN et l’ARN de thyroïdes ectopiques et orthotopiques dans lesquelles de l'expression monoallélique aléatoire dans a été observée, ce qui pourrait expliquer comment une mutation monoallélique peut avoir des conséquences pathogéniques. Finalement, le séquençage de l’exome d’une cohorte de 36 cas atteints d’HCDT a permis d’identifier de nouveaux variants probablement pathogéniques dans les gènes récurrents RYR3, SSPO, IKBKE et TNXB. Ces quatre gènes sont impliqués dans l’adhésion focale (jouant un rôle dans la migration cellulaire), suggérant un rôle direct dans les défauts de migration de la thyroïde. Les essais de migration montrent une forte diminution (au moins 60% à 5h) de la migration des cellules thyroïdiennes infectées par shRNA comparés au shCtrl dans 2 de ces gènes. Des zebrafish KO (-/- et +/-) pour ces nouveaux gènes seront réalisés afin d’évaluer leur impact sur l’embryologie de la thyroïde.

ABLE-BODIED WOMANHOOD: DISABILITY AND CORPOREALLY EXCLUSIONARY NARRATIVES IN BLACK AND WHITE WOMEN’S RIGHTS DISCOURSES, 1832-1932

This project is a feminist disability rhetorical analysis of US black and white women’s rights movements from 1832-1932. Guided by Disability and Feminist Theory, it works to identify the presence and use of patterns of disability tropes in women’s rights discourses. From Lucretia Coffin Mott to Sojourner Truth, Elizabeth Cady Stanton to Mary Church Terrell, and Charlotte Perkins Gilman to Addie Hunton, this project interrogates the rhetorical work of dominant narratives and lesser known voices in women’s rights discourses. I argue that early black and white women’s rights advocates often utilized and repeated a disability rhetoric that relied on disability metaphor, narrative prosthesis, and corporeally exclusionary narratives in order to construct definitions of womanhood. Their insistence on cognitive ability as a marker of “fitness” and “ability” provided the foundation for rights arguments based on ableist assumptions of autonomy and citizenship. I also argue that this use of disability rhetoric relied on and furthered a pervasive ableist ideology present not only in many of these movements, but in US society. In the process, US black and white women’s rights discourses have continually elided women with disabilities from women’s rights discourses because their bodies (physically, cognitively, and/or psychologically) did not meet the ableist prerequisites set for claiming women’s rights during this time period.

The Issue with Issues Management: An Engagement Approach to Integrate Gender and Emotion into Issues Management

Using sexual assault on college campuses as a context for interrogating issues management, this study offers a normative model for inclusive issues management through an engagement approach that can better account for the gendered and emotional dimensions of issues. Because public relations literature and research have offered little theoretical or practical guidance for how issues managers can most effectively deal with issues such as sexual assault, this study represents a promising step forward. Results for this study were obtained through 32 in-depth interviews with university issues managers, six focus groups with student populations, and approximately 92 hours of participant observation. By focusing on inclusion, this revised model works to have utility for an array of issues that have previously fallen outside of the dominant masculine and rationale spheres that have worked to silence marginalized publics’ experiences. Through adapting previous issues management models to focus on inclusion at the heart of a strategic process, and engagement as the strategy for achieving this, this study offers a framework for ensuring more voices are heard—which enables organizations to more effectively communicate with their publics. Additionally, findings from this research may also help practitioners at different types of organizations develop better, and proactive, communication strategies for handling emotional and gendered issues as to avoid negative media attention and work to change organizational culture.

Use of weekly assessment data to enhance evaluation of a subjective wellbeing intervention

PURPOSE: While intervention effects in target outcomes have typically been tested based on change from baseline to post-intervention, such approaches typically ignore individual differences in change, including time taken to see improvement. The present study demonstrates how weekly patient-reported data may be used to augment traditional pre-post intervention evaluations in order to gain greater insights into treatment efficacy. METHODS: Two hundred and fifty-two adolescent boys and girls (M age = 13.6 years, SD = 0.6 years) from four secondary schools in Victoria, Australia, were assigned by school into control (n = 88) or intervention (n = 164) groups. The intervention group participated in a 6-week course designed to improve subjective wellbeing (SWB) by fostering resilience, coping skills, and self-esteem. In addition to baseline, post-intervention, and 3-month follow-up assessments of SWB, intervention group participants also completed weekly summarise of affective experiences for the duration of the intervention phase. RESULTS: While standard pre-post data showed significant improvement in SWB for the intervention group relative to controls, weekly data showed individual differences in the trajectory of change during this intervention phase; low SWB individuals experienced initial worsening of symptoms followed by improvement in the second half of the intervention phase, whereas high SWB individuals experienced initial gains, followed by a plateau from Week 4 onwards. CONCLUSIONS: Addition of weekly data provided greater insights into intervention effects by: (1) contradicting the notion that early responsiveness to treatment is predictive of level of improvement by post-intervention, and (2) providing data-based insights into ways to enhance the intervention.

Early childhood science exploration: a vehicle for inclusive practices

Social justice and equity are important elements of all educational services and particularly in early childhood where there is an emphasis on including all children in the everyday life of early childhood settings. This emphasis has targeted both the policies and practices in early childhood to meet the needs of a diverse range of learners. An outcome of policy reform is the emphasis on inclusive education that is based on the right of all children to access and participate in general education. A critical pedagogy approach counters discrimination by promoting positive attitudes towards diversity. Science learning is important for all children as it is an approach to thinking and behaving that incorporates aspects of motor, behavioural, sensory, communication and mental functioning. Children from diverse situations can contribute at their own level to the opportunities involved in exploration and investigations. This paper discusses inclusive pedagogy and planning in early childhood centres with a particular focus on science learning through play and child-instigated explorations.