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Thesis (MFA)--Montana State University--Bozeman, 2008. / Typescript. Chairperson, Graduate Committee: Ronald Tobias. Sealed Off is a DVD accompanying the thesis. Includes bibliographical references (leaves 31-35).

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Le plancton représente l’ensemble des organismes qui dérivent le long des courants marins. Par sa partie phytoplancton, il produit autant d’oxygène que toutes les plantes terrestres et est, à travers le cycle du carbone, un important régulateur de la machine climatique ainsi que de l’acidité des océans. De plus, il est à la base de la chaîne alimentaire. L’écosystème planctonique joue donc un rôle important dans les équilibres nécessaires à la vie sur Terre. Pourtant, celui-ci reste peu connu. Avec le développement du séquençage haut débit et de la métagénomique, il est maintenant possible d’étudier les séquences d’ADN des micro-organismes présents dans des échantillons issus de l’océan. Le projet Tara Oceans (2009-2012) est la première expédition à avoir réalisé une collecte et un séquençage des micro-organismes planctoniques présents dans les eaux de surface à l’échelle de la planète tout en intégrant des mesures environnementales.Cette thèse consiste à étudier l’organisation génomique de l’écosystème planctonique dans les eaux océaniques de surface. Pour cela, il a été utilisé les séquences d’ADN de 644 échantillons métagénomiques correspondant à 6 fractions de taille d’organisme planctonique, allant des virus aux petits métazoaires, ainsi que les données environnementales des 113 stations Tara Oceans correspondantes. L’objectif étant de mieux comprendre dans quelle mesure l’organisation génomique et spatiale à l’échelle des individus ainsi qu’à celle des communautés micro-planctoniques est influencée par la circulation océanique et les variations environnementales.L’étude de la diversité génomique et spatiale du phytoplancton Bathycoccus prasinos a été réalisée à partir des séquences du génome de référence et d’une partie d’un second génome obtenu lors de l’expédition par une méthode d’amplification à cellule unique (SAG). La comparaison de ces deux génomes partageant la même séquence de l’ARNr 18S a révélé qu’il s’agissait de deux espèces distinctes de Bathycoccus. Une analyse de métagénomique ciblée a permis de décrire la biogéographie de ces deux écotypes qui sont présents dans des environnements différents. Enfin, cette analyse a révélé une variabilité du contenu en gènes dans les différents échantillons ce qui induit une grande plasticité génomique au sein d’une même espèce.Il est nécessaire de passer a un niveau global pour étudier l’organisation des communautés planctoniques dans les océans. La métagénomique comparative sur l’ensemble des échantillons Tara Oceans et sur les différentes fractions de tailles d’organismes permet ce passage à large échelle. L’évaluation de l’outil Compareads permettant de connaître la similarité en lectures entre deux jeux de données métagénomiques a été réalisée sur une partie des échantillons du projet Tara Oceans. Cette analyse a montré qu’il était possible avec les données métagénomiques d’étudier les modifications de la diversité génomique des communautés micro-planctoniques dans différents océans. L’analyse de la variabilité génomique le long de grands courants océaniques est alors envisageable. Un travail collaboratif pour l’amélioration de Compareads a permis le développement de l’outil COMMET qui, associé à des super calculateurs permet de réaliser les comparaisons de l’ensemble des échantillons Tara Oceans. Avec une heuristique similaire, le calcul de distances de diversité beta entre les échantillons métagénomiques a permis de proposer la première biogéographie des communautés virales, bactériennes et eucaryotes. Il a été démontré que les courants océaniques et les variations physico-chimiques ont un impact différent sur l’organisation génomique des communautés micro-planctoniques qui serait plus ou moins important selon l’échelle de temps et la taille des micro-organismes. / Plankton is composed of all organisms that drift along the currents. Through its phytoplankton part, it produces as much oxygen as all terrestrial plants and it is an important regulator of the climatic system as well as the acidity of the oceans. It is also at the base of the food web. The planktonic ecosystem plays an important role in the necessary balances for life on Earth, however it remains poorly know. With the progress of high-throughput sequencing in the last few years and with the metagenomic approach it is possible to study the DNA sequences of micro-organisms directly sampled from the ocean. The Tara Oceans expedition (2009-2012) performed a vast sampling expedition of plankton in all oceans that collected in situ environmental parameters and sequenced planktonic organisms from surface water.This thesis consists in studying the genomic organization of the planktonic ecosystem in the surface ocean waters. For this purpose, the DNA sequences of 644 metagenomic samples corresponding to 6 plankton size fractions, ranging from viruses to the small metazoan, as well as environmental data from the 113 corresponding Tara Oceans stations are used. The aim is to understand at the scale of individual organism and of global micro-planktonic communities how the genomic structure and the geographic distribution is influenced by ocean circulation and environmental variations.The study of the genomic and geographic diversity of the phytoplankton Bathycoccus prasinos was done using the sequences of a reference genome and a part of a second genome obtained during the expedition with the Single Amplification Genome method (SAG). The comparison of these two genomes sharing the same 18S rRNA revealed that they were two distinct species of Bathycoccus. A targeted metagenomic analysis helped to describe the biogeography of these two ecotypes that are present in different environments. Finally, this analysis showed variability in the gene content in samples which shows the existence of a strong genomic plasticity within species.It is necessary to scale up to global scale to study the plankton community’s organization in the oceans. The comparison of metagenomes of all Tara Oceans samples and at different size fractions of organisms allows this passage to a large scale. The evaluation of Compareads, a tool allowing us to know the similarity between two metagenomic dataset was done on a part of the Tara Oceans samples. This analysis showed the possibility to study the changes of genomic diversity of micro-planktonic communities in different oceans. Analysis of genomic variability along major ocean currents is then possible. The tool COMMET is an upgrade of Compareads which, combined with supercomputer makes it possible to carry out the comparisons of all the Tara Oceans samples. With a similar approach, the beta diversity distances between metagenomic samples made it possible to propose the first biogeography of the viral, bacterial and eukaryotic communities. It has been shown that ocean currents and physico-chemical variations have a different impact on the genomic organization of the microplanktonic communities, which would be more or less important depending on the time scale and the micro-organisms size fraction.

Density fronts are ubiquitous features of the ocean and atmosphere boundary layers. Boundary layers are characterised by strong surface fluxes of heat, water and momentum, and exhibit intense eddy fields that are associated with strong horizontal strains. Such boundary layer phenomena can drive the generation and sharpening of frontal density gradients in a process known as frontogenesis. Analytic models of frontogenesis have typically employed the `two-dimensional front' configuration where the density front is assumed to be infinitely long and straight, such that gradients along the front may be neglected, and the mathematical problem reduced to two spatial dimensions. Hoskins and Bretherton (1972) used this configuration to demonstrate how a weak background strain flow, associated with a large scale weather system, can drive the collapse of a boundary front to a discontinuity in the inviscid equations in finite time. More recently, Blumen (2000) has used the same configuration to demonstrate how an unbalanced initial state --- associated with a rapidly applied boundary flux --- can trigger an adjustment process which drives frontogenesis on the boundary. These two types of frontogenesis are known as `forced' and `spontaneous', respectively. Forced and spontaneous frontogenesis have typically been studied in isolation, despite it being well established that they can and do occur simultaneously. Furthermore, neither the Hoskins and Bretherton (1972) nor Blumen (2000) models include propagating inertia-gravity waves, despite recent observations and numerical simulations showing that these waves are often generated during active frontogenesis. Here we formulate a generalised mathematical model for the classical two-dimensional density front subject to a simple background strain flow, as studied by Hoskins and Bretherton (1972) . This model firstly unifies the disparate frontogenesis theories of Hoskins and Bretherton (1972) and Blumen (2000). Secondly, the model extends these theories by permitting arbitrary initial conditions, stratification and strong strains. Thirdly, the model incorporates non-hydrostatic effects and unbounded domains. An important novel feature of the model is the accurate description of inertia-gravity wave generation during frontogenesis. We show that these waves can be generated both by the geostrophic adjustment of initial imbalances in a stratified ambient, and spontaneously due to the acceleration of the strain flow around the front. The generalised model thus provides a unified theory capable of describing frontogenesis and wave generation in the atmosphere and ocean boundary layers on a vast range of scales. In particular, the inclusion of strong strains permits the description of frontogenesis on the ocean submesoscale. The predictions of the generalised model are confirmed by comparison with a suite of fully non-linear numerical simulations.

Coral reefs are faced and will be faced with many challenges this century. One danger is the rapid decline of oceanic pH due to anthropogenic sources. The more acidic the environment becomes, the harder reefs and coral (order: scleractinia) in particular will be hit. Experiments to measure the effect on scleractinian coral were performed to glean a better understanding of the processes that will be affected by our acidifying oceans. Additionally, the search for and analysis of coral microstructure and micromorpholgy were carried out in an attempt to understand homology within an environmentally responsive taxa.

This thesis presents a new method for controlling the look of an ocean water simulation for the purpose of creating cartoon-styled fluid animations. Two popular techniques to simulate fluid, a statistical height field method via the Fast Fourier Transform and the Stable Fluid method for dynamic effects, are connected smoothly via a blend domain, thus allowing a height field to drive a physical simulation. In addition, the height field can be stylized by utilizing a keyframing technique on wave amplitudes defined in the Fourier domain, allowing for creative control of the fluid’s surface. Such stylized height fields therefore can be simulated to exhibit natural fluid motion as well as to produce dynamic effects such as breaking waves that were previously unattainable in common fluid pipelines.

Problem formulation. The European Commission considers that health care providers and potential payers may need further evidence of mobile health (mHealth) clinical and economic benefits and despite there are hundreds of mHealth initiatives, most of them did not move beyond the pilot phase.   Purpose. This thesis aims at analyzing how can mHealth companies contribute towards solving existing health care challenges while becoming successful businesses in such an immature market. The expected results are a set of empirical evidences for companies and investors interested in this relatively new industry for the development of successful businesses, products and services.   Literature. The authors have explored classic theories and models on market entry, business and strategy development in combination with recent studies on health care, Internet and mHealth economy and ecosystem.   Methods. A qualitative multiple case study has been conducted. An analytical framework with propositions derived from the literature analysis guide the empirical study of two organizations that have successfully developed mHealth solutions in two countries with different socio-economic situations: China and Spain. Organization A is a health care and lifestyle company from Beijing responsible for a successful app with 80 million users that has brought 45 million USD investment. Organization B is the first intrapreneurial public organization born within a hospital in Madrid and committed to make knowledge available to patients and health care professionals through ICT. After a set of interviews with executive representatives and project managers, a pattern-matching analysis has been used to extract inferences and to identify correlations and deviations from literature research.   Key findings. The main conclusion of this thesis work is that mHealth is clearly a profitable blue ocean industry nowadays with lots of business opportunities to explore, room for competition and complex challenges to solve. On one side, mHealth is presented as a disruptive industry expected to cause a big impact in health care by contributing to solve costs and quality problems although there is little evidence on such benefits. On the other side, privacy, security, regulations, governments’ decisions and reluctant health care professionals become the main barriers for adoption. The outlook for the future of mHealth proves that it will be fundamental to count with multidisciplinary teams of professionals, geographically distributed health centers and technological platforms with secure and standardized communications. All these will not be possible without a general mindset change from government, administrators, regulators and health care professionals to incentivize and foster new mobile health technologies treating them as an ally rather than a threat.

Grounded theory methodology blended with action research can provide creative approaches to addressing policy-oriented questions with practical outcomes. Practical policy-oriented research outcomes are illustrated through an integrated constructivist grounded action research policy case study applied to collaborative natural resource management for Fisheries and Oceans Canada's (DFO) consideration. The study developed grounded theory, which reflexively informed collaborative strategies and supported action-oriented collaborative tool development. Outcomes were developed to address each of three research questions through cyclical reflexivity of researcher action shifts. Each action shift entailed cyclical reflexivity through re-visitation of data in light of both developed grounded theory and previous research question outcomes. As such, each question was addressed in reflexive cycles that built upon previous research outcomes, which was complimented by authorial reflexively. This constructivist grounded action bricolage demonstrates a reflexive, pragmatic, systematic approach to policy-oriented recommendations and tool development. Reflexive constructivist grounded action shift research supported strategic, integrated policy-oriented research outcomes for DFO Pacific Region's consideration. The hope of this research is to encourage further exploration of constructivist grounded action research as a dynamic, reflexive avenue that can support integrated adaptive organizational policies and management.