Variational ensemble Kalman filtering applied to data assimilation problems in computational fluid dynamics

One challenge on data assimilation (DA) methods is how the error covariance for the model state is computed. Ensemble methods have been proposed for producing error covariance estimates, as error is propagated in time using the non-linear model. Variational methods, on the other hand, use the concepts of control theory, whereby the state estimate is optimized from both the background and the measurements. Numerical optimization schemes are applied which solve the problem of memory storage and huge matrix inversion needed by classical Kalman filter methods. Variational Ensemble Kalman filter (VEnKF), as a method inspired the Variational Kalman Filter (VKF), enjoys the benefits from both ensemble methods and variational methods. It avoids filter inbreeding problems which emerge when the ensemble spread underestimates the true error covariance. In VEnKF this is tackled by resampling the ensemble every time measurements are available. One advantage of VEnKF over VKF is that it needs neither tangent linear code nor adjoint code. In this thesis, VEnKF has been applied to a two-dimensional shallow water model simulating a dam-break experiment. The model is a public code with water height measurements recorded in seven stations along the 21:2 m long 1:4 m wide flume’s mid-line. Because the data were too sparse to assimilate the 30 171 model state vector, we chose to interpolate the data both in time and in space. The results of the assimilation were compared with that of a pure simulation. We have found that the results revealed by the VEnKF were more realistic, without numerical artifacts present in the pure simulation. Creating a wrapper code for a model and DA scheme might be challenging, especially when the two were designed independently or are poorly documented. In this thesis we have presented a non-intrusive approach of coupling the model and a DA scheme. An external program is used to send and receive information between the model and DA procedure using files. The advantage of this method is that the model code changes needed are minimal, only a few lines which facilitate input and output. Apart from being simple to coupling, the approach can be employed even if the two were written in different programming languages, because the communication is not through code. The non-intrusive approach is made to accommodate parallel computing by just telling the control program to wait until all the processes have ended before the DA procedure is invoked. It is worth mentioning the overhead increase caused by the approach, as at every assimilation cycle both the model and the DA procedure have to be initialized. Nonetheless, the method can be an ideal approach for a benchmark platform in testing DA methods. The non-intrusive VEnKF has been applied to a multi-purpose hydrodynamic model COHERENS to assimilate Total Suspended Matter (TSM) in lake Säkylän Pyhäjärvi. The lake has an area of 154 km2 with an average depth of 5:4 m. Turbidity and chlorophyll-a concentrations from MERIS satellite images for 7 days between May 16 and July 6 2009 were available. The effect of the organic matter has been computationally eliminated to obtain TSM data. Because of computational demands from both COHERENS and VEnKF, we have chosen to use 1 km grid resolution. The results of the VEnKF have been compared with the measurements recorded at an automatic station located at the North-Western part of the lake. However, due to TSM data sparsity in both time and space, it could not be well matched. The use of multiple automatic stations with real time data is important to elude the time sparsity problem. With DA, this will help in better understanding the environmental hazard variables for instance. We have found that using a very high ensemble size does not necessarily improve the results, because there is a limit whereby additional ensemble members add very little to the performance. Successful implementation of the non-intrusive VEnKF and the ensemble size limit for performance leads to an emerging area of Reduced Order Modeling (ROM). To save computational resources, running full-blown model in ROM is avoided. When the ROM is applied with the non-intrusive DA approach, it might result in a cheaper algorithm that will relax computation challenges existing in the field of modelling and DA.

A Multidimensional Approach to Social Support: the Questionnaire on the Frequency of and Satisfaction with Social Support (QFSSS)

The Questionnaire on the Frequency of and Satisfaction with Social Support (QFSSS) was designed to assess the frequency of and the degree of satisfaction with perceived social support received from different sources in relation to three types of support: emotional, informational, and instrumental. This study tested the reliability of the questionnaire scores and its criterion and structural validity. The data were drawn from survey interviews of 2042 Spanish people. The results show high internal consistency (values of Cronbach's alpha ranged from .763 to .952). The correlational analysis showed significant positive associations between QFSSS scores and measures of subjective well-being and perceived social support, as well as significant negative associations with measures of loneliness (values of Pearson's r correlation ranged from .11 to .97). Confirmatory factor analysis using structural equation modelling verified an internal 4-factor structure that corresponds to the sources of support analysed: partner, family, friends, and community (values ranged from .93 to .95 for the Goodness of Fit Index (GFI); from .95 to .98 for the Comparative Fit Index (CFI); and from .10 to .07 for the Root Mean Square Error of Approximation (RMSEA)). These results confirm the validity of the QFSSS as a versatile tool which is suitable for the multidimensional assessment of social support.

Satisfying the Einstein-Podolsky-Rosen criterion with massive particles

In 1935, Einstein, Podolsky and Rosen (EPR) questioned the completeness of quantum mechanics by devising a quantum state of two massive particles with maximally correlated space and momentum coordinates. The EPR criterion qualifies such continuous-variable entangled states, where a measurement of one subsystem seemingly allows for a prediction of the second subsystem beyond the Heisenberg uncertainty relation. Up to now, continuous-variable EPR correlations have only been created with photons, while the demonstration of such strongly correlated states with massive particles is still outstanding. Here we report on the creation of an EPR-correlated two-mode squeezed state in an ultracold atomic ensemble. The state shows an EPR entanglement parameter of 0.18(3), which is 2.4 s.d. below the threshold 1/4 of the EPR criterion. We also present a full tomographic reconstruction of the underlying many-particle quantum state. The state presents a resource for tests of quantum nonlocality and a wide variety of applications in the field of continuous-variable quantum information and metrology.

Estudo de modelos simplificados com interações de longo alcance no ensemble microcanônico

Tese (doutorado)Universidade de Brasília, Instituto de Física, Programa de Pós-Graduação em Física, 2015.

Data-Driven Wildfire Propagation Modeling with FARSITE-EnKF

The goal of this study is to provide a framework for future researchers to understand and use the FARSITE wildfire-forecasting model with data assimilation. Current wildfire models lack the ability to provide accurate prediction of fire front position faster than real-time. When FARSITE is coupled with a recursive ensemble filter, the data assimilation forecast method improves. The scope includes an explanation of the standalone FARSITE application, technical details on FARSITE integration with a parallel program coupler called OpenPALM, and a model demonstration of the FARSITE-Ensemble Kalman Filter software using the FireFlux I experiment by Craig Clements. The results show that the fire front forecast is improved with the proposed data-driven methodology than with the standalone FARSITE model.

Towards the Knowledge-based Design of Universal Influenza Epitope Ensemble Vaccines

Motivation: Influenza A viral heterogeneity remains a significant threat due to unpredictable antigenic drift in seasonal influenza and antigenic shifts caused by the emergence of novel subtypes. Annual review of multivalent influenza vaccines targets strains of influenza A and B likely to be predominant in future influenza seasons. This does not induce broad, cross protective immunity against emergent subtypes. Better strategies are needed to prevent future pandemics. Cross-protection can be achieved by activating CD8+ and CD4+ T cells against highly-conserved regions of the influenza genome. We combine available experimental data with informatics-based immunological predictions to help design vaccines potentially able to induce cross-protective T-cells against multiple influenza subtypes. Results: To exemplify our approach we designed two epitope ensemble vaccines comprising highlyconserved and experimentally-verified immunogenic influenza A epitopes as putative non-seasonal influenza vaccines; one specifically targets the US population and the other is a universal vaccine. The USA-specific vaccine comprised 6 CD8+ T cell epitopes (GILGFVFTL, FMYSDFHFI, GMDPRMCSL, SVKEKDMTK, FYIQMCTEL, DTVNRTHQY) and 3 CD4+ epitopes (KGILGFVFTLTVPSE, EYIMKGVYINTALLN, ILGFVFTLTVPSERG). The universal vaccine comprised 8 CD8+ epitopes: (FMYSDFHFI, GILGFVFTL, ILRGSVAHK, FYIQMCTEL, ILKGKFQTA, YYLEKANKI, VSDGGPNLY, YSHGTGTGY) and the same 3 CD4+ epitopes. Our USA-specific vaccine has a population protection coverage (portion of the population potentially responsive to one or more component epitopes of the vaccine, PPC) of over 96% and 95% coverage of observed influenza subtypes. The universal vaccine has a PPC value of over 97% and 88% coverage of observed subtypes.

Prevalence of vocal problems in portuguese primary and secondary shool level teachers

This study compared the prevalence of vocal problems in two Portuguese groups: 73 teachers that use their voice as professional tool (teachers’ group) and 73 non-voice professionals (control group). It also identified the risk factors that contributed to teachers’ group voice problems. A questionnaire was applied to both goups in order to obtain information about vocal health, hygiene and behavior, professional activity and general physical health. Statistical results revealed that the teachers’ group presented a higher prevalence of vocal problems than the control group: 52% reported hoarseness, 46.6% vocal fatigue and 45.2% vocal discomfort compared with 31.5%, 20.5 % e 28.7%, respectively. Environmental factors (eg., smoke and cold temperatures), vocal abuse and upper respiratory pathologies (e.g., colds, laryngitis and pharyngitis) seemed to increase teachers’ voice disorders (p-value < .05). In conclusion, the absence of vocal pedagogy in the curricular plan of teachers’ higher education associated to poor working environmental conditions and professional voice demands explained the higher prevalence of vocal problems in teachers’ group.

Herramienta para mejorar la afinación vocal en Android

In this paper, a tool to improve vocal tuning in Android devices is presented. This application aims to offer exercises to practice and improve singing skills. The designed tool includes two main functionalities: sound synthesis, to provide with singing sound references, and fundamental frequency analysis, to analize the sound and check if the user sings the right musical note. The well-known Yin algorithm has been selected to perform the fundamental frequency analysis. Three different singing exercises are included: sing single notes, sing intervals and sing a note in order to complete a chord. The system also includes a graphical interface in which musical notation is employed to write down the singing sound. The system has been evaluated in order to test out its correct performance regarding both the analysis and synthesis of musical sounds.

Ensemble Stream Model for Data-Cleaning in Sensor Networks

Ensemble Stream Modeling and Data-cleaning are sensor information processing systems have different training and testing methods by which their goals are cross-validated. This research examines a mechanism, which seeks to extract novel patterns by generating ensembles from data. The main goal of label-less stream processing is to process the sensed events to eliminate the noises that are uncorrelated, and choose the most likely model without over fitting thus obtaining higher model confidence. Higher quality streams can be realized by combining many short streams into an ensemble which has the desired quality. The framework for the investigation is an existing data mining tool. First, to accommodate feature extraction such as a bush or natural forest-fire event we make an assumption of the burnt area (BA*), sensed ground truth as our target variable obtained from logs. Even though this is an obvious model choice the results are disappointing. The reasons for this are two: One, the histogram of fire activity is highly skewed. Two, the measured sensor parameters are highly correlated. Since using non descriptive features does not yield good results, we resort to temporal features. By doing so we carefully eliminate the averaging effects; the resulting histogram is more satisfactory and conceptual knowledge is learned from sensor streams. Second is the process of feature induction by cross-validating attributes with single or multi-target variables to minimize training error. We use F-measure score, which combines precision and accuracy to determine the false alarm rate of fire events. The multi-target data-cleaning trees use information purity of the target leaf-nodes to learn higher order features. A sensitive variance measure such as f-test is performed during each node’s split to select the best attribute. Ensemble stream model approach proved to improve when using complicated features with a simpler tree classifier. The ensemble framework for data-cleaning and the enhancements to quantify quality of fitness (30% spatial, 10% temporal, and 90% mobility reduction) of sensor led to the formation of streams for sensor-enabled applications. Which further motivates the novelty of stream quality labeling and its importance in solving vast amounts of real-time mobile streams generated today.

Informational masking and the effects of differences in fundamental frequency and fundamental-frequency contour on phonetic integration in a formant ensemble

This study explored the effects on speech intelligibility of across-formant differences in fundamental frequency (ΔF0) and F0 contour. Sentence-length speech analogues were presented dichotically (left=F1+F3; right=F2), either alone or—because competition usually reveals grouping cues most clearly—accompanied in the left ear by a competitor for F2 (F2C) that listeners must reject to optimize recognition. F2C was created by inverting the F2 frequency contour. In experiment 1, all left-ear formants shared the same constant F0 and ΔF0F2 was 0 or ±4 semitones. In experiment 2, all left-ear formants shared the natural F0 contour and that for F2 was natural, constant, exaggerated, or inverted. Adding F2C lowered keyword scores, presumably because of informational masking. The results for experiment 1 were complicated by effects associated with the direction of ΔF0F2; this problem was avoided in experiment 2 because all four F0 contours had the same geometric mean frequency. When the target formants were presented alone, scores were relatively high and did not depend on the F0F2 contour. F2C impact was greater when F2 had a different F0 contour from the other formants. This effect was a direct consequence of the associated ΔF0; the F0F2 contour per se did not influence competitor impact.

Satisfaction of users of primary health care with nursing care : sample of the central region of Portugal

Introdução: A satisfação dos doentes constitui um indicador indispensável para a avaliação da qualidade dos cuidados e há evidência da sua correlação com os resultados em saúde. A satisfação com os cuidados de saúde é um conceito multidimensional que considera aspetos como acesso, organização e interação doente - profissional. Consideramos que os cuidados de enfermagem, em particular, são fundamentais no processo saúde/doença. Objetivos: Validar uma escala para avaliar a satisfação dos utentes face aos cuidados de enfermagem, adaptado do instrumento EUROPEP e avaliar a satisfação dos utentes dos cuidados de saúde primários da região centro de Portugal. Material e métodos: Estudo transversal, com uma amostra de 827 utentes adultos (maioria do sexo feminino 64,4%) com uma média de idade de 50,08±18,58 anos. Os dados foram recolhidos através de um questionário, constituído por variáveis sociodemográficas, o instrumento EUROPEP (Ferreira, 1995) para avaliar a satisfação com os cuidados de saúde primários e para avaliar a satisfação especificamente com a equipa de enfermagem elaboramos questões adaptadas do instrumento EUROPEP e agrupadas nas dimensões relação de ajuda, dimensão interpessoal e instrumental. A consistência interna, reprodutibilidade e análise de conteúdo foram avaliados com recurso ao SPSS 23.0; considerando a consistência aceitável para um de Cronbach > 0,70. O coeficiente para cada item é apresentado com um intervalo de confiança de 95%. Resultados: Em todas as dimensões do questionário EUROPEP, a maior percentagem de satisfação com os cuidados situou-se entre “boa” e “muito boa”. As dimensões criadas para avaliar especificamente os cuidados de enfermagem apresentaram um coeficiente de α de Cronbach total de 0,972. Conclusões: Estes resultados sugerem que as dimensões criadas para avaliar os cuidados de enfermagem serão úteis para a investigação na população Portuguesa. A satisfação do utente é decisiva para a qualidade e eficiência dos cuidados prestados, sendo necessário o compromisso de todos os prestadores na implementação de práticas sistemáticas de gestão que conduzam à satisfação, dando particular atenção à melhoria contínua dos processos organizacionais. Palavras-chave: Satisfação dos Utentes; cuidados de saúde primários, cuidados de enfermagem, adulto, Portugal

CLASHES IN CONFINEMENT: MEN’S GENDERED EXPERIENCES WITH CONFLICT IN CANADIAN PRISONS

This dissertation presents the results of in-depth qualitative interviews with twenty-three formerly imprisoned men regarding their lived experience with prison conflict and the pain of incarceration. The results suggest that prison is a gendered ‘total institution’ (Goffman 1961). The pains that men experience in prison are uniquely gendered in that the deprivations imposed by incarceration– deprivation of autonomy, liberty, goods and services, heterosexual sex, and security (Sykes 1958) – in the reverse, define idealized masculinity as it is currently socially constructed: self-reliance, independence, toughness or invulnerability, material and economic success, and heterosexual prowess. From these shared deprivations emerges a gendered code of conduct that perpetuates a hierarchy among incarcerated men by constructing violent masculinity as a subcultural norm. The results suggest that the gender code in prison represents a set of rules that create opportunities for men to police each other’s gender performance and make claims to masculine statuses. Because status is inextricably tied to survival in this context, many men feel pressured to perform violent masculinities in prison despite privately subscribing to a non-violent sense of self-concept. The results suggest that violence is an expressive and instrumental resource for men in prison. A gender theory of prison violence, methodological findings, theoretical implications, ethical considerations and the short and long term aftermath of violent prison conflict are discussed.

Genus i ensemble : En intervjustudie om lärares syn på genusuppdraget och dess innebörd för ensembleämnet

Syftet med undersökningen är att med avseende på skolans genusuppdrag studera musiklärares förhållningsätt i ensembleundervisning på gymnasieskolan. För att uppnå detta har kvalitativa, semistrukturerade intervjuer genomförts med lärare i gymnasiekursen ensemble, följt av diskursanalys på transkriberingar av dessa intervjuer. De teoretiska utgångspunkterna är genusteorier och diskursteorier. I resultatet framkommer lärarnas syn på genusbegreppet och genusuppdraget. Bland de genusdiskurser som presenteras finns synen på genus som rutin, som sidoeffekt på annat arbete och som medvetenhet. Gällande elevsyn visar sig diskurser om eleven som platstagare, som normbrytare och vikten av att eleven känner sig som en synbar individ. Slutledningarna, liksom diskussionskapitlet, rör sig kring genusarbetets framgångar, vilka faktorer som kan ha orsakat dessa, och hur arbetet förändrats på skolorna utifrån dessa framgångar. Genomgående har ett individfokus framkommit, där eleverna inte ses som en grupp, utan som enskilda individer, vilka alla måste mötas personligt.

Do children copy an expert or a majority? Examining selective learning in instrumental and normative contexts

This study examined whether instrumental and normative learning contexts differentially influence 4- to 7-year-old children’s social learning strategies; specifically, their dispositions to copy an expert versus a majority consensus. Experiment 1 (N = 44) established that children copied a relatively competent “expert” individual over an incompetent individual in both kinds of learning context. In experiment 2 (N = 80) we then tested whether children would copy a competent individual versus a majority, in each of the two different learning contexts. Results showed that individual children differed in strategy, preferring with significant consistency across two different test trials to copy either the competent individual or the majority. This study is the first to show that children prefer to copy more competent individuals when shown competing methods of achieving an instrumental goal (Experiment 1) and provides new evidence that children, at least in our “individualist” culture, may consistently express either a competency or majority bias in learning both instrumental and normative information (Experiment 2). This effect was similar in the instrumental and normative learning contexts we applied.

Progresser dans la formation doctorale en sciences de l’humain et du social : individus et structure en tension

La présente thèse porte sur les enjeux de la progression dans la formation doctorale en sciences de l’humain et du social (SHS). Dans la plupart des pays occidentaux, les administrations universitaires se disent préoccupées par les délais d’achèvement et les faibles taux de diplomation au doctorat. S’il est admis que les aptitudes intellectuelles ne suffisent pas pour progresser dans les études doctorales, les recherches menées jusqu’ici montrent que les modalités de la formation, ainsi que le milieu et le contexte d’études dans lesquels celle-ci s’inscrit ont des répercussions sur l’expérience doctorale. Peu d’études portent toutefois sur la façon dont l’interaction de facteurs individuels et structurels peut affecter la progression dans ce processus de formation. En nous appuyant sur la théorie de la structuration de Giddens (2005), nous postulons dès lors que certaines valeurs, traditions et pratiques propres au monde académique – perpétuées, volontairement ou non, par les acteurs universitaires – peuvent nuire à la progression des doctorant-e-s. Afin d’examiner la question, une étude de cas instrumentale à visée compréhensive (Stake, 1994) a été réalisée. Six facultés des SHS d’une université canadienne ont été ciblées pour constituer le cas à l’étude. Outre l’analyse d’un ensemble de documents institutionnels relatif à la formation doctorale dans le contexte étudié, 36 doctorant-e-s issus de 19 disciplines ainsi que quatorze professeur-e-s et cinq administrateurs universitaires (directions de programmes/doyens/vices-doyens) ont été rencontrés dans le cadre d’entretiens semi-directifs. Nos résultats ont dans un premier temps permis de tracer un portrait descriptif détaillé du cas à l’étude. Les particularités de l’organisation formelle et tacite de la formation doctorale en SHS dans le contexte étudié ainsi que les défis qu’elle sous-tend ont été circonscrits, de même que les stratégies à privilégier – du point de vue des participant-e-s – pour progresser dans la formation. Dans un deuxième temps, il a été possible de montrer, d’une part, que c’est bien à la jonction de facteurs individuels et structurels que se situe la problématique de la progression dans la formation doctorale en SHS et des faibles taux de diplomation qui la caractérisent. D’autre part, la portée systémique d’une telle problématique a été mise au jour : à travers leurs choix, leurs attitudes et leurs pratiques, les acteurs universitaires contribuent à la reproduction de façon de faire et de penser « attendues » ou « admises » dans leur milieu, dont certaines ont le potentiel de nuire à la progression dans la formation doctorale.