Doctor of Philosophy / Department of Agronomy / Charles W. Rice / Soil C sequestration in agricultural ecosystems is an immediate and significant option to mitigate the increase in the atmospheric CO2 concentration. The objectives of this study were to determine 1) the influence of crop and soil management practices applicable to Kansas (i.e., tillage, N fertilization, and crop rotations) on soil C and N, C sequestration rates, soil aggregation and aggregate-associated C and N; and 2) the influence of long-term tillage practices on SOC and total N, soil aggregation and aggregate-associated C and N in three soil types: an Oxisol (Brazil), a Vertisol (Argentina), and a Mollisol (Kansas, USA). The Kansas experiments included: tillage (conventional tillage (CT), reduced tillage (RT) and no-tillage (NT)) and native prairie; nitrogen (N) fertilization rates; and crop rotations comprising various combinations of winter wheat (Triticum aestivum L.), grain sorghum (Sorghum bicolor L. Moench), and soybean (Glycine max L. Merrill). The presence of a fallow period negatively affected C sequestration rates even under NT systems. Nitrogen fertilization generally increased C sequestration rates. Rotations that contained wheat or sorghum had the greatest C sequestration rates while continuous soybean had the lowest rates. Cultivation decreased the amount of macroaggregates with a concomitment increased in the amount of microaggregates. Wheat and sorghum increased total C in the macroaggregate fraction (>250 mm) under NT while soybean had the lowest C concentration. Cultivation reduced microbial biomass C and N and potentially mineralizable C and N. The combination of conservation tillage and rotations that produced a greater amount of residue had greater C sequestration rates. In the Oxisol, NT had greater amounts of large macroaggregates (>2000 mm) than CT, however no differences between tillage practices were detected in the Vertisol and Mollisol. Cultivation of native grassland reduced the amount of macroaggregates and the associated C and N concentration; however NT tended to be more similar to the native grassland. Overall, our results indicated that the use of conservation tillage could be an important strategy to sequester C in these agroecosystems. The adoption of management practices that enhance C sequestration would be important for reducing GHGs emissions and maintaining the sustainability of agricultural systems.

Le développement de la technologie des cellules photovoltaïques organiques nécessite des compétences diverses liées à l’ingénierie moléculaire, à l’ingénierie des interfaces, au contrôle et à la caractérisation de la morphologie des films, à l’optimisation de la structure du dispositif et à la compréhension de la photo-physique des matériaux utilisés. Dans ce contexte, le travail présenté dans cette thèse contribue à la compréhension des propriétés photo-physiques des matériaux organiques π-conjugués et propose des outils de caractérisations optiques pour le suivi de la morphologie de ces matériaux. Dans un premier temps, une méthodologie rigoureuse de détermination des indices optiques des films organiques par ellipsométrie a été proposée. Les modèles utilisés en ellipsométrie ont ainsi été choisis en tenant compte des propriétés physiques des matériaux organiques π-conjugués ce qui a permis de remonter à la structure électronique de dérivés de fullèrenes (PC60BM et PC70BM). Dans un second temps, nous avons associé des données ellipsométriques à des mesures complémentaires d’absorbance et de photoluminescence dans le cas de deux copolymères (PTB7 et PTB7-Th) en films et en solutions afin d’isoler les interactions inter et intra-chaînes. Nous avons démontré que la photo-physique de ces copolymères diffère de celle du P3HT. Nous avons montré que même en solution dans le chlorobenzène, le PTB7 et le PTB7-Th s'agrègent fortement. Ces agrégats, de type H, se cassent plus facilement dans les solutions de chlorobenzène à base de PTB7-Th que dans celles à base de PTB7. / The development of organic photovoltaic cell technology requires various skills related to the molecular engineering, interface engineering, controlling and characterizing the morphology of the films, device structure optimization and understanding of photophysics of the materials. In this context, the work presented in this thesis contributes to the understanding of the photophysical properties of π-conjugated organic materials and propose optical characterizations tools for probing the morphology of these materials. First, a rigorous methodology for determining refractive indices of organic films by ellipsometry has been proposed. The models used in ellipsometry have been chosen by taking into account the physical properties of π-conjugated organic materials which allow the determination of the electronic structure of fullerene derivatives (PC60BM and PC70BM). Secondly, we associated ellipsometric data to complementary measurements of absorbance and photoluminescence in the case of two copolymers (PTB7 and PTB7-Th) in films and solutions in order to isolate inter and intra-chain interactions. We have demonstrated that the photophysics of these copolymers differs from the P3HT. We have shown that even in solution in chlorobenzene, the PTB7 PTB7-Th aggregate strongly. These aggregates, H-type, break more easily in the chlorobenzene solutions based of PTB7-Th as in those based on PTB7.

L'exposition à la chaleur, notamment lors d'incendies est particulièrement dévastatrice et dans le cas d'objets du patrimoine elle entraine la destruction de tout ou partie de ces témoins du passé. Notre étude porte sur les effets de la chaleur sur le cuir, matériau largement présent dans les collections patrimoniales.A ce jour, aucune méthode de restauration permettant d'inverser les effets de la chaleur n'a été développée. Le premier objectif de notre étude est d'évaluer les effets d'une exposition à une chaleur sèche par une caractérisation systématique d'échantillons avant et après exposition à la chaleur. Des échantillons modèles, issus d'une même peau de veau de tannage végétal connu, ont été utilisés et caractérisés à différentes échelles structurales par un large ensemble de techniques physico-chimiques et biochimiques avant et après chauffage.Au-delà du brunissement et de la rétraction visible du cuir, la chaleur induit de nombreuses altérations au niveau de la structure du matériau, notamment, une perte de masse, une fonte des structures cristallines, une augmentation de l'hydrophobie ainsi qu'une rigidification. Une partie de ces changements sont attribués à l'agrégation protéique mise en évidence par cette recherche.Le second objectif était de développer une méthode de restauration innovante basée sur l'utilisation de molécules biologiques afin de respecter la nature de l'objet. Des enzymes de type protéase, capables de rompre les agrégats protéiques ont été utilisées. Un des défis est d'apporter suffisamment d'eau, nécessaire pour l'activité de l'enzyme, sans mouiller le cuir pour éviter tout dommage supplémentaire. Plusieurs supports d'application de la protéase ont été testés. Avec une émulsion enzymatique les résultats obtenus ne mettent en évidence ni coloration, ni rétraction et dans certains cas un gain de souplesse est observé. Des résultats encourageants ont également été obtenus dans le cas d'un cuir de veau historique (XIXe siècle). Des mesures complémentaires ont fait attribuer ces propriétés principalement à l'émulsion elle-même, cependant des mesures à plus long terme semblent mettre en évidence un effet positif de l'enzyme sur le gain de souplesse. Sous réserve de nouvelles caractérisations à des temps plus longs, le traitement élaboré pourrait constituer un nouveau support de restauration par voie biologique.Mots clefs : cuir - dénaturation thermique – agrégation protéique – bio-restauration – protéases / Heat, induced by fire, is particularly devastating for cultural heritage objects as it causes the destruction of all or part of these witnesses of the past. In this study, we focused on leather, a material largely present in heritage collections. Until now, no restoration method has been developed to treat the damaging effects of heat.The first aim of our study was to evaluate the effects of dry heat on leather samples through a systematic characterization. Model samples from a calf skin vegetable tanned in known conditions were used and the consequences of heat exposure was characterized at different structural scales using a range of physical, chemical and biochemical methods.Besides the visible browning and shrinkage of leather, heat induces many changes including a loss of mass, the melt of the crystalline regions, an increase in both hydrophobicity and rigidity. Some of these changes result from the protein aggregation induced by exposure to heat and evidenced by our research.Our second goal was to develop an innovative restoration method based on the use of biological molecules in order to respect the nature of the object. Enzymes such as proteases, able to hydrolyze protein aggregates, were used. One of the challenges was to provide the water necessary for the enzyme activity without wetting the leather surface in order to avoid further damage of the leather. Several enzyme supports were tested. The use of an enzymatic emulsion reveals neither darkening nor retraction and in some cases a flexibility gain is observed. Encouraging results were also obtained in the case of an ancient book cover made from calfskin and dated from the nineteenth century. Additional measurements lead to attribute its effect mainly to the emulsion itself, however longer-term measurements appear to show a positive effect of the enzyme on the flexibility gain. Although further characterizations on the long term are required, the treatment may constitute a new support for leather bio-restoration.Keywords: leather – thermal denaturation – protein aggregation – bio-restoration - proteases

No description available.

Here I provide the first report on Geukensia granosissima patterns of abundance along a tidal gradient within a mixed mangrove stand located in Tampa Bay, Florida, USA. Specifically, I examined 1) the relationship between G. granosissima size and density with mangrove root type (e.g. prop root, pneumatophore), and of density within the intertidal zones; and 2) the possible role of predation in shaping the lower zonation patterns displayed. Transect surveys located along the lower and upper population limit boundaries were conducted every two months over a ten-month period. Variables measured include size distribution, density of mussels, above ground mangrove prop and pneumatophore roots. To evaluate potential predator influence on mussel distribution, predator exclusion experiments were conducted in March and June 2016, using mock pneumatophore platforms at both high and low tidal elevations. Surveys indicated that over all dates mean mussel densities and percent cover were higher along the lower limit tidal elevation [mean (± SD) = 1280.3 ± 665.9 m-2 and 20.6 ± 3.78% respectively], versus that in the higher limit tidal elevation [102.4 ± 50.7 m-2 and 0.52 ± 0.17%]. Survivorship of mussels in the predator exclusion platforms placed at higher position within lower edge of the mussel tidal distribution was approximately 100% on both experimental dates. During March 2016, mussel survivorship was lower when predators had access to mussels with the greatest loss of mussels in the lower (26% survivorship) vs. higher (66.5%) tidal elevations after 48h. Similarly, when predators had access to mussels in June experiments, after just 24 h mussel loss was greater at lower (1% survivorship) vs. higher (80% survivorship) tidal elevations, possibly reflecting differences in predator densities, identities, and/or functional responses. Overall trends in the patterns of distribution of this population of G. granosissima suggest that the lower tidal boundary of the mussel is shaped by predation but that predation plays a lesser role in the high tidal areas.

Le comportement d'agrégation est considéré par la majorité comme le premier pas vers des niveaux de socialité supérieurs. La compréhension des facteurs clés permettant l’émergence des décisions collectives chez les groupes composés d’individus simples (ayant une connaissance limitée de leur environnement) est fondamentale pour étudier l’évolution de la socialité. A l'heure actuelle, la majorité des études se sont focalisées sur les espèces les plus sociales et notamment celles formant des groupes monospécifiques. Les larves nécrophages de Diptères (asticots) forment sur un même cadavre des agrégats hétérospécifiques pouvant contenir des milliers d'individus leur offrant de nombreux bénéfices (production de chaleur, d’enzymes). De part ces observations in natura, ces insectes sont un bon modèle biologique dans un contexte évolutif de l'étude des comportements collectifs. Ce travail de thèse s'est attaché à mettre en évidence et quantifier les agrégations des larves de Lucilia sericata (Diptera: Calliphoridae) et les mécanismes qui sous-tendent ces regroupements. Après une description des groupes hétérospécifiques chez les arthropodes, nous avons mis en évidence pour la première fois l'existence d'un comportement d’agrégation actif des larves. Nous avons démontré l'effet d'attraction/rétention sur les larves d'un composé cuticulaire déposé au sol et reconnu par leurs congénères. Ce signal est selon nous un bon candidat comme étant l'un des vecteurs d'agrégation chez cette espèce. Cette reconnaissance se fait via l'utilisation d'un comportement exploratoire caractéristique que nous avons décrit, quantifié et nommé le scanning. Puis, nous avons mis en évidence la capacité des larves de deux espèces proches phylogénétiquement, L. sericata et Calliphora vomitoria, à faire un choix collectif pour un site de nourriture à la fois en groupe monospécifique et en hétérospécifique. Ces résultats démontrent l'existence d'une reconnaissance interspécifique des vecteurs d'agrégation (e.g. le signal larvaire) et notamment les effets d'attraction et de rétention du groupe. Enfin, nous avons mis en évidence l'existence de préférendum thermique chez ces espèces et leur capacité à sélectionner collectivement cette température préférentielle. Dans son ensemble ce travail offre des connaissances inédites sur la vie de ces groupes et notamment sur notre compréhension des phénomènes de coopération-compétition chez ces insectes d'importance en entomologie forensique (i.e. datation du décès). / Gregarism is often considered by scientists as the first step toward the most integrated societies. The understanding of the key factors that permit the emergence of collective decision in large groups composed of simple individual (having a limited knowledge of their close environment) is fundamental to decipher the evolution of sociality. Up to now, most studies are focused on highly social species and especially on those forming monospecific groups. Necrophagous larvae of Diptera (maggots) form mixed-species groups on a same decaying cadaver that can contain thousands individuals offering several benefits (heat and enzymes production). Regarding these observation in nature, these insects are an interesting biological model in the context of the study of collective behaviour. This work aimed to highlight and quantify aggregations of Lucilia sericata larvae (Diptera: Calliphoridae) and underlying mechanisms of such gathering. After an extensive review of mixed-species groups in arthropods, we highlighted for the first time an active aggregation behaviour of larvae. We demonstrated the existence of an attractive/retentive effect of a larval signal (cuticular secretion) deposit on the ground and recognize by congeners. This signal is for us a good candidate to be one of the aggregation vectors in this species. The signal recognition is made by a characteristic exploratory behaviour that we described, quantified and name scanning. Then, we demonstrated a communal collective decision-making in two related larvae species, L. sericata and Calliphora vomitoria, for one food-spot in both monospecific and heterospecific groups. These results highlighted the existence of an interspecific recognition of aggregation vectors (e.g. larval signal) especially the attraction and retention effects of the group. Finally, we demonstrated the existence of thermic preferendum species-dependent and abilities for larvae to collectively choose such temperature. This thesis work allow us new knowledges on group life of such species especially on our comprehension of cooperation-competition phenomenon in these forensically important insects (e.g. datation of the death).

Dans cette thèse, on considère la modélisation de la loi jointe des statistiques d'ordre, c.à.d. des vecteurs aléatoires avec des composantes ordonnées presque sûrement. La première partie est dédiée à la modélisation probabiliste des statistiques d'ordre d'entropie maximale à marginales fixées. Les marginales étant fixées, la caractérisation de la loi jointe revient à considérer la copule associée. Dans le Chapitre 2, on présente un résultat auxiliaire sur les copules d'entropie maximale à diagonale fixée. Une condition nécessaire et suffisante est donnée pour l'existence d'une telle copule, ainsi qu'une formule explicite de sa densité et de son entropie. La solution du problème de maximisation d'entropie pour les statistiques d'ordre à marginales fixées est présentée dans le Chapitre 3. On donne des formules explicites pour sa copule et sa densité jointe. On applique le modèle obtenu pour modéliser des paramètres physiques dans le Chapitre 4.Dans la deuxième partie de la thèse, on étudie le problème d'estimation non-paramétrique des densités d'entropie maximale des statistiques d'ordre en distance de Kullback-Leibler. Le chapitre 5 décrit une méthode d'agrégation pour des densités de probabilité et des densités spectrales, basée sur une combinaison convexe de ses logarithmes, et montre des bornes optimales non-asymptotiques en déviation. Dans le Chapitre 6, on propose une méthode adaptative issue d'un modèle exponentiel log-additif pour estimer les densités considérées, et on démontre qu'elle atteint les vitesses connues minimax. L'application de cette méthode pour estimer des dimensions des défauts est présentée dans le Chapitre 7 / In this thesis we consider the modelling of the joint distribution of order statistics, i.e. random vectors with almost surely ordered components. The first part is dedicated to the probabilistic modelling of order statistics of maximal entropy with marginal constraints. Given the marginal constraints, the characterization of the joint distribution can be given by the associated copula. Chapter 2 presents an auxiliary result giving the maximum entropy copula with a fixed diagonal section. We give a necessary and sufficient condition for its existence, and derive an explicit formula for its density and entropy. Chapter 3 provides the solution for the maximum entropy problem for order statistics with marginal constraints by identifying the copula of the maximum entropy distribution. We give explicit formulas for the copula and the joint density. An application for modelling physical parameters is given in Chapter 4.In the second part of the thesis, we consider the problem of nonparametric estimation of maximum entropy densities of order statistics in Kullback-Leibler distance. Chapter 5 presents an aggregation method for probability density and spectral density estimation, based on the convex combination of the logarithms of these functions, and gives non-asymptotic bounds on the aggregation rate. In Chapter 6, we propose an adaptive estimation method based on a log-additive exponential model to estimate maximum entropy densities of order statistics which achieves the known minimax convergence rates. The method is applied to estimating flaw dimensions in Chapter 7

Data aggregation is an important technique in wireless sensor networks. The data are gathered together by data fusion routines along the routing path, which is called data-centralized routing. We propose a localized, Delay-bounded and Energy-efficient Data Aggregation framework(DEDA) based on the novel concept of DEsired Progress (DEP). This framework works under request-driven networks with realistic MAC layer protocols. It is based on localized minimal spanning tree (LMST) which is an energy-efficient structure. Besides the energy consideration, delay reliability is also considered by means of the DEP. A node’s DEP reflects its desired progress in LMST which should be largely satisfied. Hence, the LMST edges might be replaced by unit disk graph (UDG) edges which can progress further in LMST. The DEP metric is rooted on realistic degree-based delay model so that DEDA increases the delay reliability to a large extent compared to other hop-based algorithms. We also combine our DEDA framework with area coverage and localized connected dominating set algorithms to achieve two more resilient DEDA implementations: A-DEDA and AC-DEDA. The simulation results confirm that our original DEDA and its two enhanced variants save more energy and attain a higher delay reliability ratio than existing protocols.

The need for aggregating privacy policies is present in a variety of application areas today. In traditional client/server models, websites host services along with their policies in different private domains. However, in a cloud-computing platform where aggregators can merge multiple services, users often face complex decisions in terms of choosing the right services from service providers. In this computing paradigm, the ability to aggregate policies as well as services will be useful and more effective for users that are privacy conscious regarding their sensitive or personal information. This thesis studies the problems associated with the Platform for Privacy Preference (P3P) language, and the present issues with communicating and understanding the P3P language. Furthermore, it discusses some efficient strategies and algorithms for the matching and the merging processes, and then elaborates on some privacy policy conflicts that may occur after merging policies. Lastly, the thesis presents a tool for matching and merging P3P policies. If successful, the merge produces an aggregate policy that is consistent with the policies of all participating service providers.

Red blood cells (RBCs) are the most abundant cells in human blood, representing 40 to 45% of the blood volume (hematocrit). These cells have the particular ability to deform and bridge together to form aggregates under very low shear rates. The theory and mechanics behind aggregation are, however, not yet completely understood. The purpose of this work is to provide a novel method to analyze, understand and mimic blood behaviour in microcirculation. The main objective is to develop a methodology to quantify and characterize RBC aggregates and hence enhance the current understanding of the non-Newtonian behaviour of blood at the microscale. For this purpose, suspensions of porcine blood and human blood are tested in vitro in a Poly-di-methylsiloxane (PDMS) microchannel to characterize RBC aggregates within these two types of blood. These microchannels are fabricated using standard photolithography methods. Experiments are performed using a micro Particle Image Velocimetry ( PIV) system for shear rate measurements coupled with a high speed camera for the flow visualization. Corresponding numerical simulations are conducted using a research Computational Fluid Dynamic (CFD) solver, Nek5000, based on the spectral element method solution to the incompressible non-Newtonian Navier-Stokes equations. RBC aggregate sizes are quantified in controlled and measurable shear rate environments for 5, 10 and 15% hematocrit. Aggregate sizes are determined using image processing techniques. Velocity fields of the blood flow are measured experimentally and compared to numerical simulations using simple non-Newtonian models (Power law and Carreau models). This work establishes for the first time a relationship between RBC aggregate sizes and corresponding shear rates in a microfluidic environment as well as one between RBC aggregate sizes and apparent blood viscosity at body temperature in a microfluidic controlled environment. The results of the investigation can be used to help develop new numerical models for non-Newtonian blood flow, provide a better understanding of the mechanics of RBC aggregation and help determine aggregate behaviour in clinical settings such as for degenerative diseases like diabetes and heart disease.