Global distributions of diazotrophs abundance, biomass and nitrogen fixation rates - Collection of source datasets - Contribution to the MAREDAT World Ocean Atlas of Plankton Functional Types

The MAREDAT atlas covers 11 types of plankton, ranging in size from bacteria to jellyfish. Together, these plankton groups determine the health and productivity of the global ocean and play a vital role in the global carbon cycle. Working within a uniform and consistent spatial and depth grid (map) of the global ocean, the researchers compiled thousands and tens of thousands of data points to identify regions of plankton abundance and scarcity as well as areas of data abundance and scarcity. At many of the grid points, the MAREDAT team accomplished the difficult conversion from abundance (numbers of organisms) to biomass (carbon mass of organisms). The MAREDAT atlas provides an unprecedented global data set for ecological and biochemical analysis and modeling as well as a clear mandate for compiling additional existing data and for focusing future data gathering efforts on key groups in key areas of the ocean. The present collection presents the original data sets used to compile Global distributions of diazotrophs abundance, biomass and nitrogen fixation rates

Global distributions of diazotrophs abundance and biomass - Depth integrated values computed from a collection of source datasets - Contribution to the MAREDAT World Ocean Atlas of Plankton Functional Types

The MAREDAT atlas covers 11 types of plankton, ranging in size from bacteria to jellyfish. Together, these plankton groups determine the health and productivity of the global ocean and play a vital role in the global carbon cycle. Working within a uniform and consistent spatial and depth grid (map) of the global ocean, the researchers compiled thousands and tens of thousands of data points to identify regions of plankton abundance and scarcity as well as areas of data abundance and scarcity. At many of the grid points, the MAREDAT team accomplished the difficult conversion from abundance (numbers of organisms) to biomass (carbon mass of organisms). The MAREDAT atlas provides an unprecedented global data set for ecological and biochemical analysis and modeling as well as a clear mandate for compiling additional existing data and for focusing future data gathering efforts on key groups in key areas of the ocean. The present data set presents depth integrated values of diazotrophs abundance and biomass, computed from a collection of source data sets.

Global distributions of diazotrophs nitrogen fixation rates - Depth integrated values computed from a collection of source datasets - Contribution to the MAREDAT World Ocean Atlas of Plankton Functional Types

The MAREDAT atlas covers 11 types of plankton, ranging in size from bacteria to jellyfish. Together, these plankton groups determine the health and productivity of the global ocean and play a vital role in the global carbon cycle. Working within a uniform and consistent spatial and depth grid (map) of the global ocean, the researchers compiled thousands and tens of thousands of data points to identify regions of plankton abundance and scarcity as well as areas of data abundance and scarcity. At many of the grid points, the MAREDAT team accomplished the difficult conversion from abundance (numbers of organisms) to biomass (carbon mass of organisms). The MAREDAT atlas provides an unprecedented global data set for ecological and biochemical analysis and modeling as well as a clear mandate for compiling additional existing data and for focusing future data gathering efforts on key groups in key areas of the ocean. The present data set presents depth integrated values of diazotrophs nitrogen fixation rates, computed from a collection of source data sets.

Global distributions of diazotrophs abundance, biomass and nitrogen fixation rates - Gridded data product (NetCDF) - Contribution to the MAREDAT World Ocean Atlas of Plankton Functional Types

The MAREDAT atlas covers 11 types of plankton, ranging in size from bacteria to jellyfish. Together, these plankton groups determine the health and productivity of the global ocean and play a vital role in the global carbon cycle. Working within a uniform and consistent spatial and depth grid (map) of the global ocean, the researchers compiled thousands and tens of thousands of data points to identify regions of plankton abundance and scarcity as well as areas of data abundance and scarcity. At many of the grid points, the MAREDAT team accomplished the difficult conversion from abundance (numbers of organisms) to biomass (carbon mass of organisms). The MAREDAT atlas provides an unprecedented global data set for ecological and biochemical analysis and modeling as well as a clear mandate for compiling additional existing data and for focusing future data gathering efforts on key groups in key areas of the ocean. This is a gridded data product about diazotrophic organisms . There are 6 variables. Each variable is gridded on a dimension of 360 (longitude) * 180 (latitude) * 33 (depth) * 12 (month). The first group of 3 variables are: (1) number of biomass observations, (2) biomass, and (3) special nifH-gene-based biomass. The second group of 3 variables is same as the first group except that it only grids non-zero data. We have constructed a database on diazotrophic organisms in the global pelagic upper ocean by compiling more than 11,000 direct field measurements including 3 sub-databases: (1) nitrogen fixation rates, (2) cyanobacterial diazotroph abundances from cell counts and (3) cyanobacterial diazotroph abundances from qPCR assays targeting nifH genes. Biomass conversion factors are estimated based on cell sizes to convert abundance data to diazotrophic biomass. Data are assigned to 3 groups including Trichodesmium, unicellular diazotrophic cyanobacteria (group A, B and C when applicable) and heterocystous cyanobacteria (Richelia and Calothrix). Total nitrogen fixation rates and diazotrophic biomass are calculated by summing the values from all the groups. Some of nitrogen fixation rates are whole seawater measurements and are used as total nitrogen fixation rates. Both volumetric and depth-integrated values were reported. Depth-integrated values are also calculated for those vertical profiles with values at 3 or more depths.

Pore water chemistry of samples near the sediment-water interface

Rhizon samplers were originally designed as micro-tensiometers for soil science to sample seepage water in the unsaturated zone. This study shows applications of Rhizons for porewater sampling from sediments in aquatic systems and presents a newly developed Rhizon in situ sampler (RISS). With the inexpensive Rhizon sampling technique, porewater profiles can be sampled with minimum disturbance of both the sediment structure and possible flow fields. Field experiments, tracer studies, and numerical modeling were combined to assess the suitability of Rhizons for porewater sampling. It is shown that the low effort and simple application makes Rhizons a powerful tool for porewater sampling and an alternative to classical methods. Our investigations show that Rhizons are well suited for sampling porewater on board a ship, in a laboratory, and also for in situ sampling. The results revealed that horizontally aligned Rhizons can sample porewater with a vertical resolution of 1 cm. Combined with an in situ benthic chamber system, the RISS allows studies of benthic fluxes and porewater profiles at the same location on the seafloor with negligible effect on the incubated sediment water interface. Results derived by porewater sampling of sediment cores from the Southern Ocean (Atlantic sector) and by in situ sampling of tidal flat sediments of the Wadden Sea (Sahlenburg/Cuxhaven, Germany) are presented.

Uses of agent-based modeling for health communication: the TELL ME case study

Government communication is an important management tool during a public health crisis, but understanding its impact is difficult. Strategies may be adjusted in reaction to developments on the ground and it is challenging to evaluate the impact of communication separately from other crisis management activities. Agent-based modeling is a well-established research tool in social science to respond to similar challenges. However, there have been few such models in public health. We use the example of the TELL ME agent-based model to consider ways in which a non-predictive policy model can assist policy makers. This model concerns individuals’ protective behaviors in response to an epidemic, and the communication that influences such behavior. Drawing on findings from stakeholder workshops and the results of the model itself, we suggest such a model can be useful: (i) as a teaching tool, (ii) to test theory, and (iii) to inform data collection. We also plot a path for development of similar models that could assist with communication planning for epidemics.

Contribution to the ethnobotanical study of antidiabetic medicinal plants of the Central Middle Atlas region (Morocco)

An ethnobotanical survey of medicinal plants was carried out in the Central Middle Atlas in the years 2013 and 2014 to establish the catalog of medicinal plants used in traditional medicine in the treatment of diabetes. Thus, 1560 people were interviewed, using questionnaires. The latter enabled us to gather information on traditional healing practices of the local population including scientific name, French name, vernacular name, plant parts used , therapeutic indications , revenues and mode of administration. The results show that 76 medicinal species were inventoried in the study area. These plant species are included into 67 genus and 40 families. The most represented families are: Lamiaceae (12 species), Asteraceae and Brassicaceae species with 14 each. Of 76 medicinal species found in the region, four species are reported for the first time in the traditional treatment of diabetes in Morocco. They are Pistacia atlantica, Ptychotis verticillata, Anacyclus pyrethrum, Alyssum spinosum, Cistus albidus, Juniperus thurifera, Ephedra nebrodensis, Thymus algeriensis, Th. munbyanus, Th. zygis, Abelmoschus esculentus, Fraxinus augustifolia, Sorghum vulgare and, Eriobotrya japonica. The leaves are the most used organs (38%). The decoction is the dominant mode of preparation (50%) and administration is mostly for oral use (97%).

Leave it to the Amateurs: A Career Development Explanation of Political Inexperience among Members of the Canadian Parliament:MA Thesis

In many advanced democracies, political scientists have lamented the rise of professional politicians as a challenge to the effective representation of diverse electorates. In contrast, their relative absence from Canadian federal politics gives rise to concerns over high levels of political amateurism among Canadian MPs. This study, thus, seeks to account for the numerical weakness of individuals with an occupational background in politics in the Canadian Parliament. It utilizes both individual-level quantitative data on MPs serving between the 35th and 41st Parliaments, inclusive, as well as material from qualitative interviews with over seventy former MPs. Conceptualizing the field of politics as a career in itself, and drawing on career development theory, the study finds that at the key stages of establishing, maintaining, and disengaging from a federal political career, there are specific challenges that are not significantly ameliorated by the possession of professional experience in politics itself. Professional politicians, therefore, have no major advantage over those with non-political occupational backgrounds in their career development. Furthermore, by acknowledging the existence of different types of professional politician, it finds that those whose primary occupational background was in politics itself to be in a distinct minority, but the extent of political amateurism is challenged by a much larger minority of MPs whose primary occupation was non-political but who still possess some secondary or electoral experience prior to entering Parliament.

Uses of Agent-Based Modeling for Health Communication: the TELL ME Case Study

Government communication is an important management tool during a public health crisis, but understanding its impact is difficult. Strategies may be adjusted in reaction to developments on the ground and it is challenging to evaluate the impact of communication separately from other crisis management activities. Agent-based modeling is a well-established research tool in social science to respond to similar challenges. However, there have been few such models in public health. We use the example of the TELL ME agent-based model to consider ways in which a non-predictive policy model can assist policy makers. This model concerns individuals' protective behaviors in response to an epidemic, and the communication that influences such behavior. Drawing on findings from stakeholder workshops and the results of the model itself, we suggest such a model can be useful: (i) as a teaching tool, (ii) to test theory, and (iii) to inform data collection. We also plot a path for development of similar models that could assist with communication planning for epidemics.

Recovering Natural History: Modeling Cardiovascular Biomarkers in the Presence of Endogenous Medication Use

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

Multiphase modeling of melting / solidification with high density variations using XFEM

La modélisation de la cryolite, utilisée dans la fabrication de l’aluminium, implique plusieurs défis, notament la présence de discontinuités dans la solution et l’inclusion de la difference de densité entre les phases solide et liquide. Pour surmonter ces défis, plusieurs éléments novateurs ont été développés dans cette thèse. En premier lieu, le problème du changement de phase, communément appelé problème de Stefan, a été résolu en deux dimensions en utilisant la méthode des éléments finis étendue. Une formulation utilisant un multiplicateur de Lagrange stable spécialement développée et une interpolation enrichie a été utilisée pour imposer la température de fusion à l’interface. La vitesse de l’interface est déterminée par le saut dans le flux de chaleur à travers l’interface et a été calculée en utilisant la solution du multiplicateur de Lagrange. En second lieu, les effets convectifs ont été inclus par la résolution des équations de Stokes dans la phase liquide en utilisant la méthode des éléments finis étendue aussi. Troisièmement, le changement de densité entre les phases solide et liquide, généralement négligé dans la littérature, a été pris en compte par l’ajout d’une condition aux limites de vitesse non nulle à l’interface solide-liquide pour respecter la conservation de la masse dans le système. Des problèmes analytiques et numériques ont été résolus pour valider les divers composants du modèle et le système d’équations couplés. Les solutions aux problèmes numériques ont été comparées aux solutions obtenues avec l’algorithme de déplacement de maillage de Comsol. Ces comparaisons démontrent que le modèle par éléments finis étendue reproduit correctement le problème de changement phase avec densités variables.

Hybrid mathematical and informational modeling of beam-to-column connections

The analysis of steel and composite frames has traditionally been carried out by idealizing beam-to-column connections as either rigid or pinned. Although some advanced analysis methods have been proposed to account for semi-rigid connections, the performance of these methods strongly depends on the proper modeling of connection behavior. The primary challenge of modeling beam-to-column connections is their inelastic response and continuously varying stiffness, strength, and ductility. In this dissertation, two distinct approaches—mathematical models and informational models—are proposed to account for the complex hysteretic behavior of beam-to-column connections. The performance of the two approaches is examined and is then followed by a discussion of their merits and deficiencies. To capitalize on the merits of both mathematical and informational representations, a new approach, a hybrid modeling framework, is developed and demonstrated through modeling beam-to-column connections. Component-based modeling is a compromise spanning two extremes in the field of mathematical modeling: simplified global models and finite element models. In the component-based modeling of angle connections, the five critical components of excessive deformation are identified. Constitutive relationships of angles, column panel zones, and contact between angles and column flanges, are derived by using only material and geometric properties and theoretical mechanics considerations. Those of slip and bolt hole ovalization are simplified by empirically-suggested mathematical representation and expert opinions. A mathematical model is then assembled as a macro-element by combining rigid bars and springs that represent the constitutive relationship of components. Lastly, the moment-rotation curves of the mathematical models are compared with those of experimental tests. In the case of a top-and-seat angle connection with double web angles, a pinched hysteretic response is predicted quite well by complete mechanical models, which take advantage of only material and geometric properties. On the other hand, to exhibit the highly pinched behavior of a top-and-seat angle connection without web angles, a mathematical model requires components of slip and bolt hole ovalization, which are more amenable to informational modeling. An alternative method is informational modeling, which constitutes a fundamental shift from mathematical equations to data that contain the required information about underlying mechanics. The information is extracted from observed data and stored in neural networks. Two different training data sets, analytically-generated and experimental data, are tested to examine the performance of informational models. Both informational models show acceptable agreement with the moment-rotation curves of the experiments. Adding a degradation parameter improves the informational models when modeling highly pinched hysteretic behavior. However, informational models cannot represent the contribution of individual components and therefore do not provide an insight into the underlying mechanics of components. In this study, a new hybrid modeling framework is proposed. In the hybrid framework, a conventional mathematical model is complemented by the informational methods. The basic premise of the proposed hybrid methodology is that not all features of system response are amenable to mathematical modeling, hence considering informational alternatives. This may be because (i) the underlying theory is not available or not sufficiently developed, or (ii) the existing theory is too complex and therefore not suitable for modeling within building frame analysis. The role of informational methods is to model aspects that the mathematical model leaves out. Autoprogressive algorithm and self-learning simulation extract the missing aspects from a system response. In a hybrid framework, experimental data is an integral part of modeling, rather than being used strictly for validation processes. The potential of the hybrid methodology is illustrated through modeling complex hysteretic behavior of beam-to-column connections. Mechanics-based components of deformation such as angles, flange-plates, and column panel zone, are idealized to a mathematical model by using a complete mechanical approach. Although the mathematical model represents envelope curves in terms of initial stiffness and yielding strength, it is not capable of capturing the pinching effects. Pinching is caused mainly by separation between angles and column flanges as well as slip between angles/flange-plates and beam flanges. These components of deformation are suitable for informational modeling. Finally, the moment-rotation curves of the hybrid models are validated with those of the experimental tests. The comparison shows that the hybrid models are capable of representing the highly pinched hysteretic behavior of beam-to-column connections. In addition, the developed hybrid model is successfully used to predict the behavior of a newly-designed connection.

STRUCTURAL ANALYSIS OF RIBOSOME BINDING ELEMENTS OF THE 3´ UTR IN TWO POSITIVE-STRAND PLANT RNA VIRUSES

Turnip crinkle virus (TCV) and Pea enation mosaic virus (PEMV) are two positive (+)-strand RNA viruses that are used to investigate the regulation of translation and replication due to their small size and simple genomes. Both viruses contain cap-independent translation elements (CITEs) within their 3´ untranslated regions (UTRs) that fold into tRNA-shaped structures (TSS) according to nuclear magnetic resonance and small angle x-ray scattering analysis (TCV) and computational prediction (PEMV). Specifically, the TCV TSS can directly associate with ribosomes and participates in RNA-dependent RNA polymerase (RdRp) binding. The PEMV kissing-loop TSS (kl-TSS) can simultaneously bind to ribosomes and associate with the 5´ UTR of the viral genome. Mutational analysis and chemical structure probing methods provide great insight into the function and secondary structure of the two 3´ CITEs. However, lack of 3-D structural information has limited our understanding of their functional dynamics. Here, I report the folding dynamics for the TCV TSS using optical tweezers (OT), a single molecule technique. My study of the unfolding/folding pathways for the TCV TSS has provided an unexpected unfolding pathway, confirmed the presence of Ψ3 and hairpin elements, and suggested an interconnection between the hairpins and pseudoknots. In addition, this study has demonstrated the importance of the adjacent upstream adenylate-rich sequence for the formation of H4a/Ψ3 along with the contribution of magnesium to the stability of the TCV TSS. In my second project, I report on the structural analysis of the PEMV kl-TSS using NMR and SAXS. This study has re-confirmed the base-pair pattern for the PEMV kl-TSS and the proposed interaction of the PEMV kl-TSS with its interacting partner, hairpin 5H2. The molecular envelope of the kl-TSS built from SAXS analysis suggests the kl-TSS has two functional conformations, one of which has a different shape from the previously predicted tRNA-shaped form. Along with applying biophysical methods to study the structural folding dynamics of RNAs, I have also developed a technique that improves the production of large quantities of recombinant RNAs in vivo for NMR study. In this project, I report using the wild-type and mutant E.coli strains to produce cost-effective, site-specific labeled, recombinant RNAs. This technique was validated with four representative RNAs of different sizes and complexity to produce milligram amounts of RNAs. The benefit of using site-specific labeled RNAs made from E.coli was demonstrated with several NMR techniques.

A noise simulator for eLISA: Migrating LISA Pathfinder knowledge to the eLISA mission

We present a new technical simulator for the eLISA mission, based on state space modeling techniques and developed in MATLAB. This simulator computes the coordinate and velocity over time of each body involved in the constellation, i.e. the spacecraft and its test masses, taking into account the different disturbances and actuations. This allows studying the contribution of instrumental noises and system imperfections on the residual acceleration applied on the TMs, the latter reflecting the performance of the achieved free-fall along the sensitive axis. A preliminary version of the results is presented.

A petrographic investigation into the durability of common replacement sandstones to the crystallisation of de-icing salts

Scottish sandstone buildings are now suffering the long-term effects of salt-crystallisation damage, owing in part to the repeated deposition of de-icing salts during winter months. The use of de-icing salts is necessary in order to maintain safe road and pavement conditions during cold weather, but their use comes at a price. Sodium chloride (NaCl), which is used as the primary de-icing salt throughout the country, is a salt known to be damaging to sandstone masonry. However, there remains a range of alternative, commercially available de-icing salts. It is unknown however, what effect these salts have on porous building materials, such as sandstone. In order to protect our built heritage against salt-induced decay, it is vital to understand the effects of these different salts on the range of sandstone types that we see within the historic buildings of Scotland. Eleven common types of sandstone were characterised using a suite of methods in order to understand their mineralogy, pore structure and their response to moisture movement, which are vital properties that govern a stone’s response to weathering and decay. Sandstones were then placed through a range of durability tests designed to measure their resistance to various weathering processes. Three salt crystallisation tests were undertaken on the sandstones over a range of 16 to 50 cycles, which tested their durability to NaCl, CaCl2, MgCl2 and a chloride blend salt. Samples were primarily analysed by measuring their dry weight loss after each cycle, visually after each cycle and by other complimentary methods in order to understand their changing response to moisture uptake after salt treatment. Salt crystallisation was identified as the primary mechanism of decay across each salt, with the extent of damage in each sandstone influenced by environmental conditions and pore-grain properties of the stone. Damage recorded in salt crystallisation tests was ultimately caused by the generation of high crystallisation pressures within the confined pore networks of each stone. Stone and test-specific parameters controlled the location and magnitude of damage, with the amount of micro-pores, their spatial distribution, the water absorption coefficient and the drying efficiency of each stone being identified as the most important stone-specific properties influencing salt-induced decay. Strong correlations were found between the dry weight loss of NaCl treated samples and the proportion of pores <1µm in diameter. Crystallisation pressures are known to scale inversely with pore size, while the spatial distribution of these micro-pores is thought to influence the rate, overall extent and type of decay within the stone by concentrating crystallisation pressures in specific regions of the stone. The water absorption determines the total amount of moisture entering into the stone, which represents the total amount of void space for salt crystallisation. The drying parameters on the other hand, ultimately control the distribution of salt crystallisation. Those stones that were characterised by a combination of a high proportion of micro-pores, high water absorption values and slow drying kinetics were shown to be most vulnerable to NaCl-induced decay. CaCl2 and MgCl2 are shown to have similar crystallisation behaviour, forming thin crystalline sheets under low relative humidity and/or high temperature conditions. Distinct differences in their behaviour that are influenced by test specific criteria were identified. The location of MgCl2 crystallisation close to the stone surface, as influenced by prolonged drying under moderate temperature drying conditions, was identified as the main factor that caused substantial dry weight loss in specific stone types. CaCl2 solutions remained unaffected under these conditions and only crystallised under high temperatures. Homogeneous crystallisation of CaCl2 throughout the stone produced greater internal change, with little dry weight loss recorded. NaCl formed distinctive isometric hopper crystals that caused damage through the non-equilibrium growth of salts in trapped regions of the stone. Damage was sustained as granular decay and contour scaling across most stone types. The pore network and hydric properties of the stones continually evolve in response to salt crystallisation, creating a dynamic system whereby the initial, known properties of clean quarried stone will not continually govern the processes of salt crystallisation, nor indeed can they continually predict the behaviour of stone to salt-induced decay.