Dissertations / Theses on the topic 'Dynamic linking'

The internet has facilitated music metadata production and distribution on an unprecedented scale. A contributing factor of this data deluge is a change in the authorship of this data from the expert few to the untrained crowd. The resulting unordered flood of imperfect annotations provides challenges and opportunities in identifying accurate metadata and linking it to the music audio in order to provide a richer listening experience. We advocate novel adaptations of Dynamic Programming for music metadata synchronisation, ranking and comparison. This thesis introduces Windowed Time Warping, Greedy, Constrained On-Line Time Warping for synchronisation and the Concurrence Factor for automatically ranking metadata. We begin by examining the availability of various music metadata on the web. We then review Dynamic Programming methods for aligning and comparing two source sequences whilst presenting novel, specialised adaptations for efficient, realtime synchronisation of music and metadata that make improvements in speed and accuracy over existing algorithms. The Concurrence Factor, which measures the degree in which an annotation of a song agrees with its peers, is proposed in order to utilise the wisdom of the crowds to establish a ranking system. This attribute uses a combination of the standard Dynamic Programming methods Levenshtein Edit Distance, Dynamic Time Warping, and Longest Common Subsequence to compare annotations. We present a synchronisation application for applying the aforementioned methods as well as a tablature-parsing application for mining and analysing guitar tablatures from the web. We evaluate the Concurrence Factor as a ranking system on a largescale collection of guitar tablatures and lyrics to show a correlation with accuracy that is superior to existing methods currently used in internet search engines, which are based on popularity and human ratings.

This thesis was initiated from the idea that the current static linking between learning resources imposes a limitation on e-learning applications, in particular, those applications that involve increasing resources and a diversity of learners. This situation may cause two concerns. The first concern is that learners lose the opportunity to benefit from the dynamism of available resources. Static linking limits different learners who must follow a personalised path of learning over relevant content provided by increasing and dynamic resources. The second concern involves problems of scalability in learning resource management. Statically linked resources increase the difficulty in incorporating a growing number and variety of new relevant resources. The concept of dynamic linking between learning resources is introduced to potentially overcome this limitation. The overall aim of this thesis is to develop an understanding of the requirements for producing a conceptual framework for dynamic linking between relevant resources. This framework has the two main purposes; facilitating learners in following their individual learning path over relevant resources and providing resource authors with a scalable mechanism for resource management. An iterative research approach was used during this study comprising four interrelated activities, including literature study, construction of conceptual models of human activity systems, development of a conceptual framework for dynamic linking, and prototype development and evaluation. The main outcome from this work is a conceptual framework of dynamic linking of relevant learning resources. This framework consists of high-level mechanisms that reflect the framework's functionalities. A prototype with limited functionalities was built and evaluated to demonstrate the key ideas of the framework. The conceptual framework and the prototype, along with the understanding of framework's requirements and knowledge of the system development, constitute the main contribution of this thesis.

This thesis presents a very efficient and simple approach to native code generation and dynamic code loading for the RTOS RTEMS on the Blackfin architecture. The whole solution is intended for PLCs implementing the IEC 61131-3 standard. The second part of the solution, native code loading on RTEMS, is also usable for code updates in satellite applications. For the code generation modern parser generator tools have been used to implement a language translator from Instruction List to C language. The generated C language is then feed to the freely distributable GCC compiler which generates efficient native code. This native code is later on loaded and executed on a Blackfin CPU. The execution environment RTEMS has been ported to the Blackfin architecture. RTEMS is a hard real-time operating system which has been widely used in space applications. For the dynamic loading and linking of the native code 2 different loaders have been evaluated and compared. Those loaders are of special interest for satellite applications because they allow for much faster software update over slow communication links. The final systems achieves a speedup of approximately 4 compared to a traditional interpreted IEC 61131-3 system.

It has been commonly acknowledged that in order to reach the target clienteles with loans at attractive terms and conditions, an appropriate technology for delivering financial services must be developed. Next to this, current developments in microfinance industry encourage MFIs to offer wide-ranging services within a multiservice portfolio including microsavings, microinsurance, remittances, mobile banking etc. One of the main pillars of this trend has become MFIs increasing interest in the expansion into the savings market to reach more poor clients as well as to lower costs by attracting presumably cheaper deposits. Joint services are tailored to better meet needs of the poor and aim at building sustainable financial systems and establishing closer and long-term relationship with clients. Furthermore, the rapid evolution of microfinance has generated another essential and closely related trend: commercialization. The focus of this dissertation is on three emerging issues associated with the development of microfinance sector: incentive mechanisms to address contract enforcement and screening problems, performance of MFIs though the lenses of combined microfinance services (credit plus savings), and performance of MFIs though the lenses of capital structure. The essays in the dissertation vary in research methodology: one essay is theoretical and two are empirical. Moreover, the data come from diverse microfinance units: Microfinance Information Exchange (MIX) online database and Microfinance Centre for Central & Eastern Europe and the New Independent States (MFC). As far as methods are concerned the empirical essays use less frequently applied methodologies in microfinance studies: seemingly unrelated regression (SUR) and propensity score matching (PSM).

In the context of ecological risk assessment of chemicals, individual-based population models hold great potential to increase the ecological realism of current regulatory risk assessment procedures. However, developing and parameterizing such models is time-consuming and often ad hoc. Using standardized, tested submodels of individual organisms would make individual-based modelling more efficient and coherent. In this thesis, I explored whether Dynamic Energy Budget (DEB) theory is suitable for being used as a standard submodel in individual-based models, both for ecological risk assessment and theoretical population ecology. First, I developed a generic implementation of DEB theory in an individual-based modeling (IBM) context: DEB-IBM. Using the DEB-IBM framework I tested the ability of the DEB theory to predict population-level dynamics from the properties of individuals. We used Daphnia magna as a model species, where data at the individual level was available to parameterize the model, and population-level predictions were compared against independent data from controlled population experiments. We found that DEB theory successfully predicted population growth rates and peak densities of experimental Daphnia populations in multiple experimental settings, but failed to capture the decline phase, when the available food per Daphnia was low. Further assumptions on food-dependent mortality of juveniles were needed to capture the population dynamics after the initial population peak. The resulting model then predicted, without further calibration, characteristic switches between small- and large-amplitude cycles, which have been observed for Daphnia. We conclude that cross-level tests help detecting gaps in current individual-level theories and ultimately will lead to theory development and the establishment of a generic basis for individual-based models and ecology. In addition to theoretical explorations, we tested the potential of DEB theory combined with IBMs to extrapolate effects of chemical stress from the individual to population level. For this we used information at the individual level on the effect of 3,4-dichloroanailine on Daphnia. The individual data suggested direct effects on reproduction but no significant effects on growth. Assuming such direct effects on reproduction, the model was able to accurately predict the population response to increasing concentrations of 3,4-dichloroaniline. We conclude that DEB theory combined with IBMs holds great potential for standardized ecological risk assessment based on ecological models.
Für die ökologische Risikobewertung von Chemikalien sind individuenbasierte Populationsmodelle ein vielversprechendes Werkzeug um heutige Bewertungen ökologisch realistischer zu gestalten. Allerdings ist die Entwicklung und Parametrisierung derartiger Modelle zeitaufwendig und oft wenig systematisch. Standardisierte, geprüfte Untermodelle, die Einzelorganismen beschreiben, würden die individuenbasierte Modellierung effizienter und kohärenter machen. In meiner Dissertation habe ich daher untersucht, inwieweit sich die Dynamic Energy Budget-Theorie (DEB) als Standardmodell innerhalb individuenbasierter Populationsmodelle eignet, und zwar sowohl für die ökologische Risikobewertung als auch für die theoretische Populationsökologie. Zunächst habe ich eine generische Implementierung der DEB-Theorie im Rahmen individuenbasierter Modellen (IBM) erstellt: DEB-IBM. Dieses Werkzeug nutzend habe ich dann untersucht, ob es mit Hilfe der DEB-Theorie gelingt, ausgehend von den Eigenschaften und Aktivitäten einzelner Individuen, Populationsdynamik vorherzusagen. Wir nutzten dabei Daphnia magna als Modellart, für die Daten auf der Individuenebene verfügbar waren, um das Modell zu parametrisieren, sowie Populationsdaten, mit denen Modellvorhersagen verglichen werden konnten. DEB-Theorie war in der Lage, beobachtete Populationswachstumsraten sowie die maximalen Abundanzen korrekt vorherzusagen, und zwar für verschiedene Umweltbedingungen. Für Phasen des Rückgangs der Population allerdings, wenn die für die Daphnien verfügbare Nahrungsmenge gering war, kam es zu Abweichungen. Es waren deshalb zusätzliche Annahmen über nahrungsabhängige Sterblichkeit von juvenilen Daphnien erforderlich, um die gesamte Populationsdynamik korrekt vorherzusagen. Das resultierende Modell konnte dann, ohne weitere Kalibrierungen, den für Daphnien charakteristischen Wechsel zwischen Populationszyklen mit großen und kleinen Amplituden richtig vorhersagen. Wir folgern daraus, daß Ebenen übergreifende Tests dabei helfen, Lücken in aktuellen Theorien über Einzelorganismen aufzudecken Dies trägt zur Theorieentwicklung bei und liefert Grundlagen für individuenbasierte Modellierung und Ökologie. Über diese Grundlagenfragen hinaus haben wir überprüft, ob DEB-Theorie in Kombination mit IBMs es ermöglicht, den Effekt von chemischem Streß auf Individuen auf die Populationsebene zu extrapolieren. Wir nutzten Daten über die Auswirkungen von 3,4 Dichloroanalin auf einzelne Daphnien, die zeigten daß im Wesentlichen die Reproduktion, nicht aber das Wachstum beeinträchtigt ist. Mit entsprechenden Annahmen konnte unser Modell den Effekt auf Populationsebene, für den unabhängige Daten vorlagen, korrekt vorhersagen. DEB-Theorie in Kombination mit individuenbasierter Modellierung birgt somit großes Potential für einen standardisierten modellbasierten Ansatz in der ökologischen Risikobewertung von Chemikalien.

La δ-proteobactérie Myxococcus xanthus est étudiée depuis des décennies pour sa capacité à s’auto-organiser en réponse à des stimuli environnementaux. Cette bactérie colonise des niches écologiques favorables grâce à sa capacité à se mouvoir sur des surfaces. Cette motilité lui permet d’avoir un comportement prédateur envers des organismes proies, alors qu’en absence de nutriments, elle met en place un processus développemental permettant la formation de corps fructifères contenant des myxospores résistant aux stress environnementaux. Tous ces comportements multicellulaires requièrent un contrôle dynamique de la polarité de la cellule, établi par trois protéines polaires : MglA, MglB et RomR. Ensemble, elles définissent la direction de la cellule, qui peut être rapidement inversée sous l’action du système chimiotactique Frz (réversion). Dans ce travail de thèse, à travers une approche expérimentale et computationnelle, nous avons mis en évidence que le système de régulation forme un nouveau type d’oscillateur protéique, contrôlé par deux protéines RomR et FrzX, qui agissent ensemble et de manière complémentaire pour déclencher la réversion à l’arrière des cellules. L’architecture unique de ce système permet une réponse très large à différents stimuli, essentielle pour de nombreux comportements multicellulaires. Afin de comprendre l’importance de ces transitions, nous avons mis au point un outil à haute résolution spatiale et temporelle afin de connecter les cellules individuelles aux comportements multicellulaires, et ainsi comprendre le rôle du système Frz dans un modèle multicellulaire de prédation
The δ-proteobacteria Myxococcus xanthus has been a model of study for decades for its self-organized behavior as a response of environmental stimuli. It colonizes favorable ecological niches by using surface motility. In particular, this motility allows M.xanthus to predate collectively over prey microorganisms, while under starvation they start a developmental process to form macroscopic fruiting bodies, filled with environmental resistant myxospores. All these multicellular behaviors require a dynamic control of the cell polarity established by the polarity proteins MglA, MglB and RomR. Together, they define the direction of movement of the cell, which can be rapidly inverted by the Frz chemosensory system (reversion). In this thesis work, through combined computational/experimental approaches, we highlight that the regulation system forms a new type of biochemical oscillator, controlled by two proteins RomR and FrzX, which act together through complementary action to trigger the reversion at the lagging pole. The unique architecture of this system allows a wide response to various stimuli, which could be very beneficial for collective cell behaviors. To understand the importance of these transitions, we have developed a new high-resolution single cell assay linking single cMARTINEAU EUGENIE 2018AIXM0089/016ED62 2018/03/21 62 SCES SCHell behaviors to multicellular structures at unprecedented spatial and temporal resolutions. This way, we have investigated the role of the newly identified biochemical oscillator in the multicellular model of predation

Animal behaviour is a state variable of the individual that deserves special attention given its determinant role in eco-evolutionary processes (Wolf et al. 2007 in Nature). The decomposition of the behavioural variation in between- and within-individual variability has revealed the existence of consistent between-individual differences referred to as personality or behavioural types (Dall et al. 2004 in Ecology Letters). Five axes of personality are usually recognized (exploration, aggressiveness, activity, sociability and boldness), and individual specificities along them tend to be correlated leading to what is known as behavioural syndromes. Recently, these patterns of covariation have been enlarged to accommodate movement behaviour within a personality-dependent spatial ecology theory (Spiegel et al. 2017 in Ecology Letters). Most animals tend to forage, reproduce and develop any activity within specific bounded space, which leads to the formation of home range (HR) areas (i.e., HR behaviour, Börger et al. 2008 in Ecology Letters). The increasing development of animal tracking technology is providing a huge amount of movement data revealing that HR behaviour is widespread among taxa and shows a large consistent variability, both at within- and between-individual level, which allows to define the existence of well-contrasted spatial behavioural types (SBTs). SBTs, as other personality traits, play an important role in selective processes as those impelled by harvesting activities. The Pace-of-Life-Syndrome (POLS) theory (Réale et al. 2010 in Philos. Trans. R. Soc. B Biol. Sci), hypothesises on how personality traits are expected to be correlated with life history (LH) traits along the fast-slow continuum (Stearns 1992 in Oxford Univ. Press) in the broadest sense. Accordingly, patterns of covariation between specific SBTs, physiology-related features and LHs would be expected to exist whenever they maximize the animal performance in a given environment. However, the way in which behavioural variation at the within-species level is translated to the wide range of LH traits remains a fundamental yet unresolved question, mainly due to the lack of a proper theoretical framework (Mathot & Frankenhuis, March 2018 in Behavioral Ecology and Sociobiology). Thus, unrevealing the mechanisms behind is certainly scientifically very exciting but also socially relevant. In such a context, this PhD thesis aimed to address from conceptual, empirical and theoretical perspectives cornerstone questions in behavioural ecology: what are the feasible mechanisms underpinning the establishment of HR areas and within-species variation, what are their consequences for animal functioning and performance (i.e., in. LH traits) at the individual and eco-evolutionary levels, or what are the implications for the assessment and conservation of wildlife of the existence of SBTs. The PhD thesis focusses in a fish heavily exploited by recreational fishers but it aims to provide general reasoning applicable to a wide range of wild animals. First, the PhD thesis proposes a mechanistic theory of personality-dependent movement behaviour based on dynamic energy budget models (i.e., a behavioural-bioenergetics theoretical model). Second, integrated in the field of animal personality (i.e., decomposition of behavioural variability into within- and between-individual’s components), it addresses empirically the study of behavioural variability in the main axis of personality for a marine fish species and looked for evidences of whether personality-mediated differences in energy acquisition may exist. Aiming to support empirically the possible connections between personality traits and space-use behaviour, the thesis provides some insights on the application of a novel-tracking algorithm to analyse the movement of individual fish submitted to different experimental conditions. Third, it provides two examples of how applying HR-related theoretical concepts may improve the management of natural resources: attending the properties of HR may facilitate the assessment of wildlife using fixed monitoring sampling stations, and considering SBTs may influence the assessment of the status of wild fish stocks. Finally, the adaptive value of the proposed behavioural-bioenergetics theory is explored by means of dynamic optimization to understand the eco-evolutionary consequences related with HR variability. In summary, this PhD thesis makes an important contribution to behavioural ecology by developing a unifying theory to test the generality and adaptive value of POLS based on dynamic energy budgets. This behavioural-bioenergetics model connects (1) personality traits (2) HR behaviour, (3) physiology and (4) LH traits through an interwoven of mass/energy fluxes, within which they interact and feedback with the ecological context. Overall, from an eco-evolutionary perspective, the proposed framework constitutes a powerful tool for exploring the ecological role of HR behaviour and predicting what combination of behavioural traits would be evolutionally favoured in a given ecological context. Moving forward to including managerial scenarios, this unifying theory provides scientifically founded knowledge that would promote to improve natural resource management by attending the behavioural component of animal populations.

This dissertation proposes the Weaves runtime framework for the execution of large scale parallel programs over lightweight intra-process threads. The goal of the Weaves framework is to help process-based legacy parallel programs exploit the scalability of threads without any modifications. The framework separates global variables used by identical, but independent, threads of legacy parallel programs without resorting to thread-based re-programming. At the same time, it also facilitates low-overhead collaboration among threads of a legacy parallel program through multi-granular selective sharing of global variables. Applications that follow the tenets of the Weaves framework can load multiple identical, but independent, copies of arbitrary object files within a single process. They can compose the runtime images of these object files in graph-like ways and run intra-process threads through them to realize various degrees of multi-granular selective sharing or separation of global variables among the threads. Using direct runtime control over the resolution of individual references to functions and variables, they can also manipulate program composition at fine granularities. Most importantly, the Weaves framework does not entail any modifications to either the source codes or the native codes of the object files. The framework is completely transparent. Results from experiments with a real-world process-based parallel application show that the framework can correctly execute a thousand parallel threads containing non-threadsafe global variables on a single machine - nearly twice as many as the traditional process-based approach can - without any code modifications. On increasing the number of machines, the application experiences super-linear speedup, which illustrates scalability. Results from another similar application, chosen from a different software area to emphasize the breadth of this research, show that the framework's facilities for low-overhead collaboration among parallel threads allows for significantly greater scales of achievable parallelism than technologies for inter-process collaboration allow. Ultimately, larger scales of parallelism enable more accurate software modeling of real-world parallel systems, such as computer networks and multi-physics natural phenomena.
Ph. D.

Content: Fish collagen has been considered to be an alternative for mammalian collagen, however, physicochemical properties of fish collagen-based materials such as gels are so far not adequate for actual application. In the present study, we prepared two types of fish collagen gels with sufficient elasticity: i) dehydrated fibrillogenesis collagen gels (DFCG), which were fabricated via collagen self-assembly followed by immersion in different concentrations of ethanol solutions, and ii) dehydrated cross-linking collagen gels (DCCG), which were fabricated via collagen self-assembly and simultaneous cross-linking followed by immersion in ethanol solution. Furthermore, the physicochemical properties of DFCG and DCCG were analyzed by atomic force microscopy, differential scanning calorimetry, enzymatic degradation and dynamic viscoelastic measurements. The microstructure of DFCG was consisted of characteristic Dperiodic collagen fibrils and insusceptible of ethanol concentrations (20-100% (v/v)). However, the thermal stability, remaining weight after enzymatic degradation and mechanical properties of DFCG distinctly increased with the increase of ethanol dose, possiblely ascribing that ethanol with higher polarity might dehydrate partial free water of DFCG and strengthen the interactions of hydrogen bond. Especially, for the gel treated by 100% (v/v) enthanol, Td increased by 32.7 °C and G′ was 55-folds than those of undehydrated gel (43.1 °C and 239.2 Pa). In the case of DCCG, the formation of collagen fibrils was depended on the concentrations of N-hydroxysuccinimide adipic acid derivative (NHS-AA), which was converted to [NHS-AA]/[NH2] ratios (calculated by the [active ester group] of NHS-AA and [ε-NH2] of lysine and hydroxylysine residues of collagen). As the ratio= 0.05, the characteristic D-periodic fibrils were still formed and the treatment of 60% (v/v) ethanol increased the Td (52.5 °C) and G′ (7388 Pa) values of the gel compared with those of uncross-linked gel (49 °C and 2064.32 Pa, respectively), majorly resulting from the effects of covalent cross-linking bonds and hydrogen bonds. However, when the ratio= 0.2, the collagen self-assembly was intensively inhibited and the dehydration of free water within gel structure in the absence of thick fibrils led to the shrinkage of the gel and an obvious decrease in Td (42 °C) and G′ (432 Pa). Although the [NHS-AA]/[NH2] ratio further increased to 0.8, the thermal stability and elasticity of the gel enhanced mildly suggesting that the presence of thick fibrils formed via the self-assembly was significantly crucial for reinforcing the gels. Take-Away: The fish collagen gels with excellent elasticity were prepared via the treatment of ethanol. The physicochemical properties of the dehydrated gels were depended on the concentrations of ethanol. The presence of characteristic D-periodic fibrils was significantly crucial for reinforcing the gels.

The extent and dynamics of permafrost are tightly linked to the distribution and movement of water in arctic landscapes. As the Arctic warms more rapidly than the global average, profound changes are expected in both permafrost and hydrology; however, much is still not known about the interactions between these two systems. The aim of this thesis is to provide new knowledge on the links between permafrost and hydrology under varying environmental conditions and across different scales. The objectives are to (i) determine how permafrost distributions and patterns in morphology are linked to hydrology, (ii) determine how groundwater flow influences ground temperature dynamics in permafrost landscapes, and (iii) explore the mechanisms that link permafrost to groundwater and streamflow dynamics. A range of methods have been applied within the four studies (papers I-IV) comprising the thesis: geophysical (ground penetrating radar and electrical resistivity tomography) and GIS techniques for mapping and analyzing permafrost distributions and related morphology; numerical modeling of coupled heat and water fluxes for mechanistic understanding permafrost-hydrological links; and statistical analyses for detecting trends in streamflow associated with permafrost thaw. Combining these various methods here allows for, and may be considered a prerequisite for, novel insights to processes. The thesis also presents statistical analyses of field observations of ground temperatures, ground- and surface water levels, as well as lake and shore morphological variables. Discontinuous permafrost peatlands are heterogeneous environments regarding permafrost distributions and thickness which is manifested in surface systems such as lake geometries. In these environments, lateral groundwater fluxes, which are not considered in most permafrost models, can significantly influence ground temperature dynamics, especially during high groundwater gradient conditions. River discharge data provide a potential for monitoring catchment-scale changes in permafrost, as the magnitude and seasonality of groundwater fluxes feeding into streams are affected by the distribution of permafrost. This thesis highlights the need to understand water and permafrost as an integrated system with potential internal feedback processes. For example, permafrost thaw can lead to increases in groundwater discharge which in turn can lead to increased heat transfer through the ground, resulting in further acceleration of permafrost thaw rates.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.

This project takes advantage of molecular dynamic simulation for the design of polymer nanocomposites. The newly synthesized low-dimensional carbon nanomaterials show unlimited potential in enhancing the mechanical performance of the polymer. The atomistic simulation approach enables a comprehensive characterization approach for the materials down to atomic level and establish in-detail insights into their mechanical behaviors usually beyond the reach of experiments. The obtained results and analysis establish a fundamental understanding of the enhancement mechanisms for the nanoscale reinforcements in polymer nanocomposites, which could eventually guide their design, fabrication, and engineering implementation.

Mitochondrial cytochrome c (Cc) is a small haem protein, primarily involved in electron transfer, but is an example of an extreme multifunctional protein with roles in several stages of apoptosis through interaction with phospholipids and Apaf-1. The switch in function is associated with an interaction with cardiolipin (CL) and gain of peroxidase activity. Mutations in the Cc gene lead to Thrombocytopenia 4, a disease associated with enhanced apoptotic activity. The Y48H variant is found in the 40-57 W-loop, the lowest free-energy foldon. A 1.36 Å resolution X-ray structure of the Y48H variant reveals minimal structural changes to that of the wild-type protein and G41S variant (also associated with Thrombocytopenia 4). Despite this, the intrinsic peroxidase activity is enhanced, implying that a penta-coordinate haem species is more prevalent in the Y48H variant, corroborated through determination of a Met80 off-rate of > 125 s-1 compared with ~ 6 s-1 for the wild-type protein. Heteronuclear NMR experiments with the ferric Y48H variant have revealed heighted dynamics relative to the WT protein in the 40-57 and 71-85 W-loops, the latter being the loop containing the Met80 ligand, suggesting communication between these two substructures. When these results are considered in relation to the G41S variant, a dynamic picture emerges in which heightened dynamics in key substructures of the Cc fold facilitate an increased population of a penta-coordinate, peroxidase active species of the order wild-type < G41S < Y48H. Studying the alkaline transition through pH jump stopped-flow 2 spectroscopy has revealed that not only is the pK695 is reduced by ~ 1 pH unit compared to that of the wild-type protein, but also the pK of the trigger is lowered. In contrast, variants in the 71-85 W-loop do not alter the pK of the trigger but are nevertheless associated with enhanced peroxidase activity relative to the wild-type protein, due to enhanced local dynamics within the haem crevice.

Much progress has been made in developing a precautionary approach to fisheries management, however in most cases, this has been largely confined to biological elements and a more balanced application needs to address social and economic risks as well. A current challenge for global fisheries governing bodies is to manage fishing capacity so that it is commensurate with the availability of the resource. Fisheries science is by its nature an interdisciplinary field, and combining information has proven to be increasingly important in achieving sustainable fisheries management. One factor of increasing importance is the ability to anticipate fisher behaviour in response to management regulation, in order to reduce the unanticipated side effects of management actions aimed both at the fishery sector and at other sectors. The primary aim of this work is to improve understanding of fisher behaviour to support fisheries management. Statistical modelling tools were applied to determine the relative importance of, and improve understanding of, selected drivers for both short term and long term behavioural responses to fishery management measures, to quantify the relationships between capacity, effort and fishing mortality and to investigate spatial competition with other marine sectors. The results demonstrate that expected revenues from target species, experience or habit, management measures, fuel prices, aggregate activity and maritime traffic are significant factors in determining fisher decision-making on when and where to fish. Some of the unobserved random components of the model causing heterogeneity in the selection of fishing grounds by fishers could be attributable to individual variations in decision-making, along with other factors such as skipper skill, age, nationality and vessel attributes. Detailed individual-level vessel data that take into account the heterogeneity and dynamics of a beam-trawl fishing fleet were analysed to draw linkages between capacity, effort and fishing mortality. These relationships could be developed for use as indicators for spatial and temporal management. A key finding from this study was the detection of a switch in species targeting and fishing efficiency over time, with an estimated 6.2% annual decrease in plaice (Pleuronectes platessa) and an estimated 0.6% increase in sole (Solea solea) over the 11-year study period. The research demonstrated how knowledge of drivers of fisher behaviour can lead to better understanding of responses of fishing fleets to management and how more detailed information on fleet structure and dynamics (including effort and capacity) improves knowledge of the relative contributions of different components of a fleet to fishing mortality.

Linking environmental variation to population dynamics is necessary to understand and predict how the environment influences species abundances and distributions. I used demographic, environmental and trait data of forest herbs to study effects of spatial variation in environmental factors on populations as well as environmental change in terms of effects of forest succession on field layer plants. The results show that abundances of field layer species during forest succession are correlated with their functional traits; species with high specific leaf area increased more in abundance. I also found that soil nutrients affect vegetative and flowering phenology of the forest herb Actaea spicata. The effect of nutrients shows that a wider range of environmental factors than usually assumed can influence plant phenology. Moreover, local environmental factors affected also the demography of A. spicata through effects on vital rates. An abiotic factor, soil potassium affecting individual growth rate, was more important for population growth rate than seed predation, the most conspicuous biotic interaction in this system. Density independent changes in soil potassium during forest succession, and to a lesser extent plant population size dependent seed predation, were predicted to alter population growth rate, and thereby the abundance, of A. spicata over time. Because these environmental factors had effects on population projections, they can potentially influence the occupancy pattern of this species along successional gradients. I conclude that including deterministic, as opposed to stochastic, environmental change in demographic models enables assessments of the effects of processes such as succession, altered land-use, and climate change on population dynamics. Models explicitly incorporating environmental factors are useful for studying population dynamics in a realistic context, and to guide management of threatened species in changing environments.

Over time, small local disturbances may result in large regional changes in landscape structure and function. For example, lightning strikes may lead to large-scale wildfire or land clearing to urbanization. In either case, landscape patterns change as the type and distribution of landscape elements change in response to disturbances. Additionally, changes in landscape patterns often affect ecological processes. For example, wildfires and urbanization affect succession and productivity, which changes the distribution of habitat features, and which may affect landscape connectivity for species inhabiting the landscape. I used rank-size distributions and their scaling exponents to illustrate landscape character and change in Yellowstone National Park and a portion of the metropolitan area of Tucson, Arizona, through patterns associated with the distribution of patch size. I found that natural and anthropogenic disturbances affected landscape organization similarly and thus produced similar distributional patterns of patch size. However, the magnitude of change created by natural and anthropogenic disturbances differed. Fires in Yellowstone National Park produced scaling exponents >1, suggesting that large patches affected the distribution of patch size disproportionately. Comparatively, urbanization in the Tucson metropolitan area produced scaling exponents ≈1, suggesting that large and small patches affect the distribution of patch size proportionately. To link changes in landscape patterns with changes in ecological processes I compared four commonly used landscape metrics with rank-size distributions and their scaling exponents. Rank-size distributions described the scaling properties of the landscape with regard to patch size, whereas other metrics did not. This is meaningful because there is an integral relationship between scaling properties of the landscape and scaling properties of species using the landscape. A species may perceive a landscape as connected when the patch-size characteristics of the landscape scale proportionally with the body-size characteristics of the species. As a result, the species may be more likely to move through and therefore persist in that landscape. I develop a theoretical relationship between natural and anthropogenic disturbances, describe landscape organization, and link landscape and species scaling characteristics.

This Ph.D. thesis investigates Earth’s dynamic evolution through geological time by addressing possible linkages between the evolution of the Earth’s mantle and crustal growth, plate tectonics, and superplume-supercontinental cycles. This is achieved through deciphering the geochemical records of mantle-derived/related rocks that characterised the Earth’s mantle evolution and processes at global-, regional- and micro- to nano-scales.

Considerable effort has been dedicated to restoring sturgeon habitat within dammed rivers. However, sedimentation causes long-term failure because interstitial voids provide critical habitat during early life-stages. Based on the premise that a better understanding of geomorphic processes will improve restoration design, this study characterizes flow and sediment transport dynamics through a white sturgeon spawning reach on the Nechako River, BC. An extensive dataset was collected throughout the 2015 flood. Bedload transport was sampled on 36 days with flows ranging from 44 m³/s to 656 m³/s. During a high flow of 525 m³/s, channel bathymetry and water surface elevation were surveyed and velocity profiles were collected across 9 transects. Banklines, bars and island topography were later surveyed during low flow. Sediment transport into the reach was positively related with discharge. This relation was non-linear and transport rates increased rapidly once flows exceeded 400 m³/s. The relation weakened with downstream distance and sediment transport peaked progressively later throughout the year. No relation was observed at the downstream end of the reach, where transport rates remained low and constant relative to upstream. Sediment was primarily transported through secondary channels conveying a disproportionate amount of sediment compared to flow. Within the single-thread channel, the locations conveying the greatest amount of sediment remained spatially consistent over time. Hydrodynamic modelling indicates the Burrard Ave. Bridge causes backwatering once discharge exceed 225-275 m³/s. Velocity, shear stress and transport capacity at the downstream end of the reach do not increase with discharge because of the backwatering and the expansion in channel width through the island complex. The locations of maximum shear stress and transport capacity shift upstream with increasing discharge, but shear stress does not exceed 23 N/m² for flows up to 775 m³/s. The fluvial dynamics within the spawning reach create challenges and opportunities for habitat restoration. Backwatering is problematic because it causes mid-reach deposition during high flows and limits shear stress magnitude over the downstream spawning substrate. Meanwhile, the presence of sediment transport pathways through secondary channels and within the mainstem can be used to site restoration projects in areas apt to maintain suitable habitat.
Arts, Faculty of
Geography, Department of
Graduate

The ravages of influenza in humans and mammals are well documented and the subject of considerable interest. There is extensive research on influenza infection in small animal models. Less is known of the dynamics of infection in natural hosts, however, research on experimental equine influenza in horses provides an exception. Following an overview of the uses and applications of models at both scales, chapter 2 reviews in detail the biology of equine influenza. Outlining the known pathology and immunology, it presents a picture of the within host viral dynamics using data from experimental equine influenza infections in horses. A model is constructed to capture the within-host dynamics of equine influenza in chapter 3 and is shown to capture the pattern of viral dynamics in both naive and previously exposed hosts. This model of individual disease dynamics is then incorporated into a population framework. It is found that including more biological realism in terms of individually determined disease dynamics does not result in epidemics that differ significantly from those predicted by standard models of influenza dynamics. The infections caused by the morbilliviruses are, like influenza, acute, highly transmissible infections. They provide a number of interesting contrasts, however, particularly in their response to vaccination. The population dynamics of the morbilliviral infections are amongst the most well studied and a series of studies on the pathogenesis of rinderpest infection in cattle provides a good picture of the within-host dynamics of morbilliviral infection. The systemic nature of morbilliviral infections and the pathogenesis of rinderpest is described in chapter 5. A model is constructed to capture its dynamic and is found to describe well the dynamics in naive hosts. In contrast to influenza, incorporating rinderpest dynamics into population models resulted in herd level dynamics that were distinct to those predicted by SEIR models, the longer incubation period of morbilliviruses appearing to have a significant impact.

The purpose of this research is to investigate the interactions between organizational effectiveness, quality culture, and employee health. The system dynamics modeling approach is used in order to reveal the complex and dynamic behavior of the system under investigation. Understanding system behavior facilitates policy analysis and management decision-making. The relationships between the three constructs: organizational effectiveness, quality culture and employee health are non linear and during the research a number of dynamic hypotheses were investigated. For example, illness is the main cause for absenteeism, loss of productivity, ineffective learning, which in turn causes even more stress and eventually more illness. As part of the system dynamics approach a conceptual (qualitative) model and a formal (quantitative) model were built. The conclusion from analyzing the dynamic hypotheses of this model was that quality culture had a great impact on the performance of the whole system, especially on employees’ health and on organizational effectiveness. Furthermore, employees’ health and organizational effectiveness concurrently impact each other. However, this research could not show a considerable impact of the employees’ health and organizational effectiveness on the organization’s quality culture. The research contributes to the general understanding of complex production systems, since the three constructs investigated in this research face similar issues, i.e., the trade-off between long-term and short-term goals, consequences of managerial actions that are far apart in time and space, and conflicts between measurable outcomes and subjective outcomes. The research adds to the design of effective social systems, where the products and the services are created in a quality fashion, and individuals experience an environment that is conducive to their well-being.
Ph. D.

Recently, epoxy polymers have been used in different applications and research fields due to their superior properties. In this study, the classical molecular dynamics (MD) was used to simulate formation of the epoxy polymer from cross linking of the EPON 828 with DETA curing agent, and calculate the glass transition temperature (Tg) of the material. A series of MD simulations were independently carried out on the cross-linked epoxy polymer in a range of temperatures from 600 K down to 250 K, and the density of the materials was calculated at the end of each run. Through the linear fitting between temperature and density above and below the glass transition temperature, Tg was estimated. The glass transition temperature of the pure DGEBA were also estimated through the same procedure and compared with those of the cross-linked polymer. Molecular simulations revealed significant increase in Tg of the cross-linked epoxy polymer as a result of newly created covalent bonds between individual chains. When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/35102

Accelerated soil erosion affects sustainable food production through the degradation of arable soils resulting in lower crop yields and compromising biodiversity. Over the past 50 years, the weed seedbank has been declining due to farming intensification, increased herbicide use and weed suppression through competitive autumn crop planting. However, there is less recognition of the potential of soil erosion affecting the weed seedbank. This thesis contributes to an improved understanding of the effect of geomorphological processes (soil erosion) on biological systems (weed seedbank) in arable ecosystems. The first investigation assessed whether the management of farm machinery field tramlines would decrease soil erosion rates and effect the movement of weed seeds. Over three winter seasons, eroded material was collected by a network of Gerlach Troughs. The results showed that tramline management with a spiked harrow decreased soil and seed loss by 93.9% and 86.56% respectively, compared to regular tyre tramlines. Analysis of seed data to runoff and sediment load found seeds were transported along with sediment (r²=0.62) rather than runoff (r2=0.2) over the long term. In addition, tramline management significantly affected the number of seed species transported (p<0.001), which was found to relate to seed morphologies. Overall, tramlines cause 0.01% - 0.32% seed fluxes annually depending on management. These findings have implications for farmers to protect tramlines from erosion and displace seeds through management thereby, preventing the loss of biodiversity within the field. The second investigation looked at the movement of weed seeds at the field scale by erosion through the use of a radionuclide (¹³⁷Cs) tracer. A single field was sampled for seedbank and soil cores taken for ¹³⁷Cs analysis in two sub field grids. The results indicated weak relationships between seedbank densities and erosion. The weak relationships in the grids (r² =0.13, p =0.029 in 2011 and r² =0.12, p = 0.036) were due to land management contributing to spatial variability within seedbank abundance and composition. Individual species showed mixed responses to erosion rates. The findings indicate farmers need to consider management strategies at field scale to effectively manage erosion and seedbanks because seedbank losses of between 2 – 2.5 % annually within the field which is linked to field scale sediment budgets. The third investigation looked at specific environmental controls that would affect soil erosion and seedbanks. This was achieved by using a portable rainfall simulator on plots containing either seeds from the natural seedbank or spiked with seeds. The key control was the presence of crop/vegetation cover in affecting erosion rates (p<0.001) and seed movement (p = 0.001). The presence of crop cover resulted in low erosion rates but a greater loss of seeds compared to plots with no crop cover. This was linked to vegetation cover providing a protective environment for weeds to grow and produce additional seeds via seed rain. Ground cover prevents erosion but also highlighted seed movement was higher than on bare soil due to a greater availability. This means that surface wash is more important than rainfall in causing seed transport. For spiked plots, more seeds were displaced in short (3 minute) events compared with long (6 minute) events (p = 0.04). This shows protecting the soil and seedbank from rainfall detachment is crucial to preventing transport of sediment and seeds that could enter other transport pathways (e.g. tramlines, rills, gullies). The fourth investigation looked into the processes and impacts of soil erosion on seedbanks at the catchment scale. This was done by establishing a monitoring station at the outlet of an arable catchment for one year to monitor discharge, suspended solids and seed flux. The results of monitoring in 2012 found seeds numbers were positively related to discharge (observed r² = 0.62, p<0.001; observed plus modelled r²=0.50, p <0.001) and sediment load (observed r² = 0.64, p<0.001; observed plus modelled r2= 0.89, p<0.001). Seed species had poor negative relationships with discharge (observed r² = 0.03, p=0.357; observed plus modelled r²=0.11, p = 0.017) and sediment load (observed r² <0.001, p=0.352; observed plus modelled r²=0.14, p=0.004). An initial estimate of losses from the catchment was around 0.008 – 0.027% of the weed seedbank. Interestingly, there appeared to be a trend in the abundance of seed collected relating to patterns of farming activity within the catchment. This finding has management implications as there is evidence, for the first time, of arable weed seeds being exported from the catchments, which could affect other agricultural land and ecosystems downstream. The findings of these four investigations showed that the effect of soil erosion on the seedbank is connected at different spatial scales. Scope for future work is to improve the understanding of the role of seed morphologies, land management and field scale processes affecting the transportability of seeds by erosion processes.

The Florida Everglades is a massive and highly managed subtropical wetland ecosystem, strongly influenced by anthropogenic control of freshwater distribution and highly susceptible to a changing climate, including rising sea-level and changes in temperature and rainfall. Shifting hydrologic regimes impact ecosystem function and biogeochemistry, which in turn control the sources, fate, and transport of organic matter. As a master environmental variable, it is essential to understand how organic matter dynamics will respond to changes in the balance between freshwater and saltwater associated with landscape-scale Everglades restoration efforts and climate change. The research comprising this dissertation improves current understanding of the linkages between organic matter and hydrology in the Everglades across a broad range of temporal and spatial scales. A range of research tools, including stable molecular biomarkers, water quality sensors, data synthesis and multivariate statistics were utilized. Biomarkers were used to track particulate organic matter mobilization in response to experimentally manipulated flows and provided initial evidence that sheet flow restoration can re-engineer landscape microtopography, influencing both ecosystem structure and organic matter inputs to Everglades National Park (ENP). Short-term and long-term temporal studies indicated the quantity and quality of dissolved organic carbon responds to changes in freshwater flow to marshes and mangrove forests in ENP, and that spatial patterns and trends are driven by a complex mixture of managed and natural surface water inputs (i.e., rainfall and water management inflows) as well as groundwater discharge. Application of climate scenario forecasting to relationships established between organic matter and hydrologic drivers predicted reductions in dissolved organic carbon export from ENP and changes in organic matter molecular composition. Furthermore, high-frequency measurements showed hydrologic connectivity of freshwater and estuarine organic matter pools at sub-monthly time-scales. In summary, the work presented here clearly indicates strong yet spatiotemporally complex relationships between changes in water and the sources and transport of organic carbon through the Everglades.

The host immune response against infection requires the coordinated action of many diverse cell subsets that dynamically adapt to a pathogen threat. Due to the complexity of such a response, most immunological studies have focused on a few genes, proteins, or cell types. With the development of “omic”-technologies and computational analysis methods, attempts to analyse and understand complex system dynamics are now feasible. However, the decomposition of transcriptomic data sets generated from complete organs remains a major challenge. Here, we combined Weighted Gene Coexpression Network Analysis (WGCNA) and Digital Cell Quantifier (DCQ) to analyse time-resolved mouse splenic transcriptomes in acute and chronic Lymphocytic Choriomeningitis Virus (LCMV) infections. This enabled us to generate hypotheses about complex immune functioning after a virus-induced perturbation. This strategy was validated by successfully predicting several known immune phenomena, such as effector cytotoxic T lymphocyte (CTL) expansion and exhaustion. Furthermore, we predicted and subsequently verified experimentally that virus-specific CD8+ T cells with an early effector transcriptome profile participate in the host adaptation to an overwhelming virus threat. Thus, the linking of gene expression changes with immune cell kinetics provides novel insights into the complex immune processes within infected tissues.
La respuesta inmune del huésped contra una infección requiere la acción coordinada de varios tipos de células que, de forma dinámica, se adapta a la amenaza del patógeno. Debido a la complejidad de dicha respuesta, la mayoría de los estudios inmunológicos se han centrado en pocos genes, proteínas o en células específicas. Con el desarrollo de tecnologías "ómicas" y métodos de análisis computacionales, los intentos de analizar y comprender sistemas complejos ahora son más factibles. Sin embargo, la descomposición de datos de transcriptomas, generados a partir de órganos completos sigue siendo un desafío importante. Aquí he combinado Weighted Gene Coexpression Network Analysis (WGCNA) y Digital Cell Quantifier (DCQ) para analizar los perfiles transcriptómicos de bazos de ratón, a diferentes tiempos, durante la infección aguda y crónica por el virus de la Coriomeningitis Linfocítica Aguda (LCMV). Este método nos ha permitido generar hipótesis sobre funcionamiento del complejo sistema inmune después de una perturbación inducida por el virus. Esta estrategia fue validada al predecir con éxito varios fenómenos inmunes conocidos, como la expansión de los linfocitos T citotóxicos (CTL) y el fenómeno conocido como agotamiento. Además, he predicho y posteriormente verificado de forma experimental que las células efectoras T CD8+ específicas de virus, con un perfil de transcriptoma efector temprano, participan en la adaptación a la amenaza del virus. Por lo tanto, la conexión entre la expresión de genes y la cinética de las células del sistema inmune, proporciona nuevos conocimientos sobre los complejos procesos inmunes en tejidos infectados.

Critical Source Areas (CSAs) of phosphorus (P) are areas within a watershed that have a high propensity to export P to surface waters. CSAs contain two factors: source and transport factors. Source factors include soil P status and fertilizer and manure inputs, while transport factors include hydrologic and erosion processes that mobilize P. The aim of this study was to: 1) identify CSAs of P in an agricultural watershed and the stormflow dynamics controlling P export and 2) to delineate CSAs of P at the agricultural field scale using georeferenced soil test P (STP) and a digital elevation model (DEM) in a geographic information system (GIS). Soil test P (STP) along with dissolved reactive P (DRP), particulate P (PP), and total P (TP) in soil water, groundwater, and surface runoff were monitored in three small (< 8 ha) agricultural watersheds located in Decatur, Illinois, each situated within a separate experimental field. Further, volumetric water content (VWC) was continuously monitored on topographic positions, e.g. foot slopes, hill slopes, and shoulder slopes, to determine topographic position influence on soil moisture distribution. Repeated measures mixed models analysis showed that foot slopes (32.2%) had significantly higher VWC than hill slope (29.6%) and shoulder slopes (30.9%) during the growing season, while foot slopes (38.9%) and hill slopes (38.9%) had significantly higher VWC than shoulder slopes (34.9%) during the dormant season. Persistent shallow groundwater tables were implicated to control spatial and temporal VWC moisture distribution. Both foot slopes and hill slopes were implicated as transport areas. Repeated measures mixed models analysis also showed that foot slopes (73 kg ha&minus1) had significantly higher STP than hill slopes (28.9 kg ha&minus1) and shoulder slopes (33.8 kg ha&minus1) most likely due to the erosion and deposition of sediment from upper slopes to lower slopes. Foot slopes were consequently classified as source areas. A surface runoff event revealed near stream saturation and flushing of soil moisture from upper slopes to lower slopes, indicating that the watersheds are variable source area driven. The peak of PP on the rising limb of the hydrograph was attributed to near stream sediment mobility while the peak of DRP on the falling limb was attributed to flushing of upper slope soil moisture via subsurface flow. GIS delineation of CSAs at the agricultural field scale was conducted to pinpoint precise locations within a field to implement precision P management. The topographic position index (TPI) along with a modified version of the slope classification model &mdash both of which were created by Weiss (2001) and automated by Jenness (2006) &mdash were used to delineate foot slopes, hill slopes, shoulder slopes, and flat areas within a 91.2 ha agricultural field from a DEM. Transport factors were, again, identified as foot slopes and hill slopes. Further, georeferenced STP data collected in spring 2010, fall 2010, and fall 2011 were averaged and interpolated using ordinary kriging to generate a single surface that represented three year spatial soil P status within the agricultural field. Source factors were identified as areas in the field that were excessive in soil P for corn-soybean production. A CSA model was created that identified areas where both source factors and transport factors overlapped. CSAs of P occurred on 2.3 ha of the agricultural field and occurred near grass waterways and roadside drainage ditches. A one way analysis of variance (ANOVA) along with a Tukey mean separation procedure of soil P on the four topographic positions was used to characterize soil P spatial dependencies on landscape attributes associated with topographic position. Foot slopes (79.5 kg ha&minus1) and flat areas (92.9 kg ha&minus1) had significantly greater soil P than hill slopes (59.8 kg ha&minus1) and shoulder slopes (49.8 kg ha&minus1) due to depositional and sink attributes. Depositional attributes exhibit concave curvature, e.g. foot slopes. This curvature effectively reduces the velocity of surface runoff so that sediment bound P suspended in surface runoff can be deposited on the soil surface. Sink areas accrue P inputs but do not lose P to erosion via surface runoff. These areas exhibit linear, non-sloping planes, e.g. flat areas, that are not conducive to surface runoff. Although topographic position explains the spatial dependencies of source and transport factors, the CSA model was able to pinpoint where CSAs of P spatially occur within the agricultural field which can allow for precision P management.

Birds are one of the best studied animal groups in the world but are also amongst the most endangered. The wealth of ecological information has shown habitat protection to be vital to bird biodiversity, but habitat loss and degradation continue to defeat conservationists.
Community-based biodiversity conservation efforts have been recently recognized as an important option for safeguarding ecosystems while reducing land use conflicts arising from the material, cultural and spiritual needs of local inhabitants. Community involvement is particularly critical for conservation in anthropogenic habitats. Few studies have linked the ecological impacts of community land use practices with the auto-ecological requirements of dependent bird species. In this study I examine the conservation possibilities for the endangered Sierra Madre sparrow (Xenospiza baileyi) by considering three basic elements: the ecological requirements of the bird, the effects of traditional land use practices in shaping the habitat, and the economic and social conditions that influence current and future land use decisions. I draw on ecological field studies, on traditional ecological knowledge systems, and studies of the political ecological context that influences local practices.
The studies were carried out from 2000-2003 and employed a combination of ethnographic, participative and spatial-ecological approaches to address human-land interactions and their impacts on the sparrow habitat. Social data were obtained through nine workshops which included site visits, transect walks, participatory mapping, oral histories and semi-structured interviews. Ecological data were obtained from landscape ecology analysis, vegetation post-disturbance assessments and detailed bird's nest-site selection analysis.
Results indicate that local people, principally herders, hold a rich knowledge of fire use to achieve diverse purposes, including pasture renewal, grassland maintenance and grass species selection, and prevention of dangerous fires. In order to accomplish their goals, herders have established rotational fire and grazing regimes that consider timing, frequency, location and extent of these disturbance-based practices. This rotational system was found to benefit the Sierra Madre sparrow by maintaining the grassland at the scales needed by the sparrow for nesting. Multiscale habitat recommendations for the species' conservation were derived from this socio-ecological interaction and dynamics.
Unfortunately, external conservation perspectives and interests and internal land tenure conflicts have altered this rotational regime and local perspectives on resource management that threaten the resilience of this social-ecological system. Consequently, traditional ecological knowledge on grassland management can be on risk of disappearing and, with it, important native grasses and grasslands are being made vulnerable. The survival of the Sierra Madre sparrow in particular and of associated biodiversity in general, is in peril if these conflicts are not solved in a relatively short time. A community-based fire co-management program is recommended to promote integrative bird conservation-local development scenarios.

Freezing stress is detrimental to plants, resulting in major crop losses in temperate regions. The plant cell wall is a dynamic network of proteins and polysaccharides including cellulose, hemicellulose and pectins. It is essential for plant survival, providing structural integrity, strength and protection against pathogens. As the cell wall is the site of ice formation, it has also been suggested that the wall could contribute towards protection of the plant against freezing damage. The cell wall undergoes remodelling during cold acclimation, but it is unclear what specific role this restructuring may play in freezing tolerance. The sensitive to freezing8 (sfr8) mutant contains less cell wall fucose due do a mutation in the fucose biosynthetic gene MUR1. This was shown to result in a decrease in dimerisation of the cell wall pectic domain rhamnogalacturonan-II (RG-II), which in wild type plants is predominantly dimerised via a borate-ester cross-link. This decrease in dimerisation likely results in the observed freezing sensitivity of mur1 mutants, as supplementation of plants with boric acid was shown to restore freezing tolerance. Guard cell dynamics were also compromised in the sfr8 mutant, as stomata were found to be more restricted in their movements than wild type in response to ABA, CO2 and changes in humidity. The freezing and guard cell phenotypes of sfr8 may be attributed to a decrease in the tensile modulus of the cell wall with reduced RG-II dimerisation. This makes the wall more vulnerable to deformation during freezing and prevents the guard cells from stiffening to allow an increase in stomatal aperture. RG-II dimerisation also mediates certain structural aspects of the cell wall that may facilitate supercooling by excluding ice nucleation and preventing ice growth. This research reveals the importance of RG-II dimerisation in cell wall dynamics and the impact cell-wall composition has on freezing and desiccation tolerance. These findings could lead to the identification of new targets for crop breeding.

Les individus varient en termes de taux de survie et de taux de reproduction. Les variations de ces taux vitaux peuvent être reliées aux caractéristiques des individus tel que la masse et l’âge. Des modèles démographiques ont été développé pour prendre en compte ces variations dans les populations naturelles et permettre de faire des prédictions pour gérer les populations naturelles. Cependant, la quantité de données démographiques nécessaire pour construire ces modèles n’est pas disponible dans toutes les populations. Pour surmonter ce problème, j’ai pendant ma thèse décrit les patrons généraux des relations reliant l’âge et la masse aux taux vitaux chez les mammifères et les oiseaux. En utilisant les données de la littérature, j’ai pu décrire les patrons généraux de ces relations et mis en évidence les facteurs biologiques pouvant expliquer les variations de ces relations entre les espèces et les populations. Dans un premier temps je me suis concentrer sur le lien entre la masse des individus et leurs taux vitaux. J’ai montré un effet positif de la masse des jeunes sur la survie des jeunes. J’ai ensuite mis évidence l’effet des différentes causes de mortalité sur cette relation avec par exemple un effet négatif de la prédation sur l’intensité de cette relation. J’ai ensuite montré un effet positif de la masse de la mère sur la masse du jeune et enfin que la probabilité de reproduction d’une femelle est impactée positivement par sa masse. Dans une seconde partie, je me suis concentré sur le lien entre l’âge et la survie chez les mammifères. Pour décrire ce lien, nous avons construit une base de données MALDDABA compilant les relations reliant l’âge aux taux vitaux chez les populations naturelles de mammifères que nous avons extraits de tables de vie issues de la littérature. En utilisant ces données, nous avons démontré que les femelles vivent en moyenne plus longtemps que les mâles chez les mammifères en milieu naturelles. J’ai enfin décrit les avantages at les inconvénients des différentes métriques de longévité et proposé de nouvelles méthodes pour décrire la relation entre l’âge et le taux de mortalité. Avec cette thèse, je mets en avant l’utilisation des approches comparatives pour mieux comprendre quels sont les facteurs qui influence la dynamique des populations naturelles
Individuals varies in terms of survival and reproduction. Most of those variations in vital rates can be linked to individual characteristics such as age or body mass. Demographic models were developed to make prediction on those trait-structured populations and are now often used to manage wild populations. However, the amount of data needed to perform those models is not available for every populations. To overcome this issue, I tried in my thesis to assess the general patterns for the relationships linking age and body mass to the vital rates in birds and mammals. By comparing relationship extracted in the literature, I was then able to assess the general effect of body or age on vital rates as well as the biological factor explaining the variation of those relationships between species and populations. I first assess how body mass influence vital rates in birds and mammals. I demonstrated the positive effect of offspring body mass on offspring survival and showed how the relative importance of each causes of mortality influence this relationship, with for instance a negative effect of the predation rate on the intensity of the relationship. I also showed that mother body mass is positively related to offspring body mass and that heavier mother are also more likely to reproduce. On a second part I focused on describing the relationship between age and survival for mammals. We built a database MALDDABA compiling all relationships linking vital rates to age for wild mammals from life tables reported in the literature. Using life table data compiled in the database I was able to demonstrate that females live on average longer than males in wild populations of mammals. I then critically assess the metrics of longevity and provide new insight to describe the relationship between mortality and age. With my thesis I provided new views on the uses of comparative approach to highlight the major factors influencing the population dynamic in the wild

Mining for the recovery of minerals and coal can result in acid mine drainage (AMD) which presents an environmental risk. Acid mine drainage, as the name suggests, is acidic run-off water from mostly mine waste dumps. It affects water quality by lowering its pH and increasing its metal and sulphate loading, thus making it unsuitable for use by many forms of life. AMD must therefore be treated before entering nearby water systems and soils. An effective treatment technology is considered as the one that can result in water neutralisation and removal of metals and sulphate. Biological sulphate reduction (BSR) technologies, mediated by sulphate reducing bacteria (SRB), have attracted attention as a sulphate remediation strategy as they offer a cheap alternative to other sulphate removal technologies such as chemical approaches. In addition, the concomitant generation of alkalinity and soluble sulphide assist in neutralisation and heavy metal removal. One of the challenges associated with BSR is the supply of a cost-effective carbon source which also acts as an electron donor for the anaerobic reduction of sulphate. Studies have reported that both the choice of carbon source and electron donor and the microbial communities present influence the sulphate reduction process, the former frequently defining technoeconomic feasibility. The feed sulphate concentration and residence time, together defining the volumetric sulphate loading rate, have also been reported to influence the efficacy of the sulphate reduction process and needs to be optimised for the microbial community present and the chosen electron donor. The identification and characterisation of the microbial communities involved and investigating how these change with changes in operating conditions is crucial in the optimisation of BSR processes. Currently, there are no commonly used molecular tools which can be used for routine analysis of SRB communities in real time and on a regular basis and cost effectively. This makes it difficult to understand the link between changes in the mixed BSR microbial community structure and process performance. The study presented in this thesis had three main objectives. Firstly, to evaluate the use of an anaerobic digestate, obtained from a partially anaerobically digested Cyanobacteria species (Arthrospira platensis, commonly known as Spirulina), as a carbon source and electron donor for BSR. Secondly, to validate, optimise and apply the molecular tools for analysis of the relative abundances of species within the mixed BSR microbial community in this study. Thirdly, to compare the microbial community dynamics and performance of BSR using the complex anaerobic digestate as carbon source and electron donor to BSR using a single electron donor source, lactate. Chemostat studies using a mixed SRB consortium were carried out using anaerobic digestate, characterised as containing a mixture of acetate, propionate and butyrate, as a carbon source and electron donor for BSR. Upon reaching steady-state, the concentrations of sulphate, bicarbonate, acetate, propionate and butyrate were measured and used to estimate the BSR kinetics and reaction stoichiometry. A 16S rRNA gene survey of the BSR inoculum used for this thesis was performed by constructing a 16S rRNA gene clone library and analysis of the diversity of clones was performed using amplified ribosomal DNA restriction analysis (ARDRA). These 16S rRNA sequences were used to provide insight into the diversity and phylogenetic relatedness of the bacterial community and key species within the mixed BSR inoculum. In silico analysis of the 16S rRNA sequences captured from the clone library was performed to design novel genus specific quantitative real-time PCR (qPCR) primers and to validate the specificity of previously published primers. Fluorescence in situ hybridisation (FISH) techniques were optimised for the visual characterisation of this microbial community. FISH and qPCR were then applied to assess how the mixed microbial community structure was affected by the changes in the volumetric sulphate loading rate (VSLR), mediated through dilution rate and feed sulphate concentration, when anaerobic digestate (mixed carbon source) and lactate (simple carbon source) were used as an electron donor for BSR. The results obtained were used to examine and compare the link between microbial community dynamics and performance of sulphate reducers between the mixed and the simple carbon source. The results obtained from this thesis suggested the simultaneous utilisation of all the three volatile fatty acids (acetate, propionate and butyrate) present in anaerobic digestate which contributed to the robustness of the chemostat reactors as indicated by higher sulphate, propionate and butyrate conversion efficiencies. The kinetic profiles of the volumetric sulphate reduction rate (VSRR) obtained with anaerobic digestate were well matched with the kinetics observed in previous studies when single carbon sources and electron donors were used for BSR. At a feed sulphate concentration of 1.0 g l-1 , the oxidation of acetate, propionate and butyrate and concomitant sulphate reduction were observed across the dilution rates of 0.0083 to 0.083 h -1 . The stoichiometry of BSR utilising propionate and butyrate as carbon and electron donor suggested that by increasing feed sulphate concentrations from 1.0 to 2.5 and 5.0 g l-1 acetogenic reactions were favoured at the higher dilution rates of 0.042 and 0.083 h-1 . However, increasing the feed sulphate concentration at the lower dilution rates of 0.0083 to 0.021 h-1 did not alter the oxidation of volatile fatty acids (VFAs) and concomitant sulphate reduction, suggesting that the sensitivity of the propionate and butyrate oxidisers was related to specific growth rate rather than the sulphate loading. A previous mathematical model developed by Moosa et al. (2002) was used to determine microbial growth constants (μmax and Ks) and energetic coefficients (Yx/s) for SRB at each feed sulphate concentration to describe the microbial growth kinetics obtained with anaerobic digestate. A 16S rRNA gene survey, performed by 16S rRNA library construction and 16S rRNA gene amplicon sequencing, revealed a more diverse microbial community in the inoculum obtained from a lactate operated BSR reactor than previously reported. qPCR was used to confirm the presence and relative abundance of these species within the reactors receiving anaerobic digestate or lactate as carbon source and electron donor. The 16S rRNA sequences captured were found to have high similarity to well- known SRB species belonging to the Desulfomicrobium, Desulfovibrio, Desulfuromonas, Desulfobulbus and Desulfocurvus genera. Other “non-traditional SRB” species belonging to the Firmicutes and Citrobacter genera containing a specific molecular target for the detection of SRBs, the dissimilatory sulphite reductase gene (dsrAB), within their genomes were also detected. DsrAB is the key enzyme catalysing the last and main energy-generating step during sulphate reduction. Non-SRB species present were identified as members of the Sphaerochaeta, Synergistetes, Chloroflexi, Mesotoga, Acholeplasma, Bacteriodetes, Petrimonas and Bacteriodes genera. A 16S rRNA gene survey by 16S rRNA variable region amplification from metagenomic DNA extracted from microbial biomass associated with continuous stirred tank reactors (CSTRs) operated on anaerobic digestate or lactate was performed to validate the qPCR results and assist with the identification of the “other SRB” and nonSRB species. The 16S rRNA gene survey suggested the presence of 13 known SRB species Desulfomicrobium groups (Desulfomicrobium hypogeium and Desulfomicrobium aestuarii), Desulfovibrio species (D. aminophilus, D. vulgaris, D. desulfuricans, D. intestinalis, D. oxamicus, and D. sulfodismutans), Desulfobulbus oligotrophicus, Desulfocurvus vexinensis, Desulfococcus biacutus, Desulfarculus baarsii, Desulfomonile tiedjei and Desulfobacca acetoxidans in CSTRs operated on anaerobic digestate. Only up to 10 SRB species, Desulfomicrobium hypogeium, Desulfomicrobium aestuarii, Desulfovibrio groups (Desulfovibrio aminophilus, Desulfovibrio vulgaris, Desulfovibrio desulfuricans, Desulfovibrio intestinalis, Desulfovibrio sulfodismutans, Desulfovibrio mexicanus, Desulfobulbus oligotrophicus and Desulfocurvus vexinensis were observed in reactors with lactate, suggesting that the multiple VFAs present in the anaerobic digestate (acetate, propionate and butyrate) were able to support a more diverse SRB community than a single electron donor (lactate). Various non-SRB bacterial genera as well as known elemental sulphur reducing bacteria Desulfuromonas acetexigens and Dethiosulfovibrio acidaminovorans were also found to be present, with the latter being associated only with the lactate operated reactor. qPCR results indicated that despite being present in high proportions at the lowest VSLRs, the Desulfomicrobium species were washed out of the reactors at higher VSLRs regardless of carbon source and electron donor was provided. Species from the Desulfovibrio genera, which were present at lower abundances than the Desulfomicrobium species, were more resistant to changes in dilution rates and remained present within the reactors at the higher VSLRs, 0.104 and 0.208 g l-1 h -1 . In the reactors operated on anaerobic digestate, the decline in the abundance of Desulfovibrio species at VSLRs of 0.052 and 0.104 g l-1 h -1 , correlated with a noticeable decline in sulphate conversion from 60.4 to 49.4% at feed sulphate of 2.5 g l-1 , and from 66.9 to 22.6% at feed sulphate of 5.0 g l-1 . These findings suggest that Desulfovibrio species may play a critical role in sustained sulphate reduction at lower VSLRs. 16S rRNA gene amplicon data validated the qPCR data showing that increasing the VSLR, resulted in a change in the SRB community structure and a decrease in the proportion of total SRB within the microbial community. In agreement with the FISH and qPCR findings, Desulfomicrobium hypogeium was identified as the most abundant operational taxonomic unit (OTU) belonging to SRB present at the lowest dilution rate (D) tested (0.0083 h-1 , retention time (RT = 1/D) of 5 d) when anaerobic digestate was used as an electron donor for BSR. Washout of most SRB species was also observed when the dilution rate was increased from 0.0083 to 0.042 h-1 (RT of 5 to 1 d) in these reactors. Species such as Desulfovibrio sulfodismutans, Desulfomonile tiedjei, the acetate oxidiser Desulfococcus biacutus and the elemental sulphur reducing Desulfuromonas acetexigens were found to tolerate higher VSLRs of 0.104 and 0.208 g l-1 h -1 (dilution rate of 0.042 h-1 ), suggesting fast enough growth rates to remain in these reactors at the higher dilution rate of 0.042 h-1 . A decrease in the abundance of the incomplete propionate oxidiser Desulfobulbus oligotrophicus correlated to a decrease in propionate oxidation at a VSLR of 0.104 and 0.208 g l-1 h -1 suggesting that this SRB was responsible for the oxidation of propionate and concomitant sulphate reduction observed in these reactors. Similar to the reactors receiving anaerobic digestate, increasing the dilution rate from 0.0083 to 0.042_h -1 (RT of 5 to 1 d) resulted in washout of most SRB OTUs in CSTRs operated on lactate. At a feed sulphate concentration of 10.0 g l-1 , increasing the dilution rate from 0.0083 to 0.042 h-1 resulted in an increase in the proportion of the lactate oxidiser Desulfocurvus vexinensis from 25 to 98% of the total SRB proportion. At this dilution rate (0.042 h-1 ), other SRB species observed were the lactate oxidisers Desulfovibrio sulfodismutans and Desulfobulbus oligotrophicus which can oxidise lactate and the product of its incomplete oxidation, propionate. Although the abundance of these two SRB at the dilution rate of 0.042 h-1 was much lower than that of Desulfocurvus vexinensis, studies with anaerobic digestate suggested Desulfobulbus oligotrophicus which was abundant at only 0.004% and was identified as the only propionate degrader in the CSTR resulted in propionate conversion of 21.7%. This suggested that the less abundant Desulfovibrio sulfodismutans and Desulfobulbus oligotrophicus may have also played a role in sulphate reduction at the dilution rate of 0.042 h-1 in the CSTR with lactate. In addition, Desulfocurvus vexinensis and Desulfobulbus oligotrophicus were able to function at a VSLR of 0.42 g l-1 h -1 which suggests these two SRB species could be used effectively to reduce sulphate to hydrogen sulphide in wastewaters with higher VSLRs of up to 0.42 g l-1 h -1 when lactate was provided as an electron donor for BSR. The acetate specialist, Desulfobacca acetoxidans, the butyrate oxidiser Desulfarculus baarsii and the propionate oxidiser Desulfobulbus oligotrophicus, were able to function at a VSLR of 0.208 g l-1 h -1 suggesting that a combination of these three SRB species could be used in BSR treatment processes with VSLRs of up to 0.208 g l-1 h -1 where anaerobic digestate is provided as an electron donor. The ability for anaerobic digestate to support diverse SRB communities even at higher VSLRs may add to the robustness of the reactors to maintain sulphate reduction even at high VSLRs. This thesis showed that both the presence and diversity of SRB species are subject to the carbon source and VSLR. To the author's knowledge, this is the first study to indicate the relationship between the change in SRB community structure and sulphate reduction performance when anaerobic digestate (a complex carbon source) is used as a carbon source and electron donor for BSR. Results from this thesis suggest that the use of a mixed volatile fatty acid stream generated for the partial digestion of a suitably digestible biomass may be used as electron donor and carbon source to support a robust BSR process for the treatment of AMD. Using a mixed volatile fatty acid stream also has potential to result in the development of a more economically viable AMD treatment process.

Die Gattung Daphnia nimmt eine zentrale Position im pelagischen Nahrungsnetz vieler Standgewässern (Seen, Talsperren) ein. Aufgrund hoher Filtrierleistungen sind Daphnien für das integrierte Gewässermanagement, z.B. im Rahmen einer Nahrungskettenmanipulation (Biomanipulation), von großem Interesse. Ihre relativ einfache Kultivierbarkeit machte sie außerdem zu einen weit verbreiteten Modellorganismus limnologischer Grundlagenforschung. Das Ziel dieser Arbeit besteht darin, ein umfassendes Modellsystem für die Gattung Daphnia zu entwickeln, das wesentliche Kenntnisse der Ökologie von Daphnia miteinander verknüpft, um eine Vernetzung des Wissens zu realisieren. Bestehende Modellansätze konnten diese Aufgabe nur unzureichend erfüllen, weil sie in der Regel einem &quot;Problem-orientierten Ansatz&quot; folgen und somit sehr unterschiedliche inhaltliche Ausrichtungen und verschiedene Modellstrukturen aufweisen. Eine Kopplung bzw. ein direkter Vergleich dieser Modelle ist deshalb in der Regel schwierig. Dieses Modellsystem wurde entwickelt, um ein Instrument zur Synthese des vorhandenen Prozesswissens bereitzustellen, und nicht, um ein spezifisches, abgegrenztes Problem zu bearbeiten; es steht somit diametral zu existierenden Ansätzen. Aus diesem Grunde wird der gewählte Ansatz als ein &quot;Spezies-orientierter Ansatz&quot; bezeichnet. Drei Eigenschaften charakterisieren diesen Ansatz. (i) Das Modellsystem umfasst mehrere hierarchische Ebenen biologischer Organisation, wobei der Schwerpunkt auf den Ebenen des Individuums und der Population liegt. Interaktionen zwischen diesen Organisationsebenen sind ausgeprägt und in Feld- und Laborstudien gut belegt, in existierenden Modellen aber noch unzureichend miteinander verknüpft. (ii) Da eine quantitative Interpretation der Ergebnisse beabsichtigt ist, wurden die Modellausgaben einer umfangreichen Validation an unabhängigen und bereits publizierten Daten unterzogen. (iii) Das Modellsystem zeichnet sich durch einen geschachtelten Aufbau aus (nested design), wodurch eine einfache Erweiterbarkeit des Modells oder auch die separate Anwendung bestimmter Modellkomponenten gewährleistet ist
The scope of this thesis was to develop a comprehensive model system of the genus Daphnia, a key organism in the pelagic food web of lakes and reservoirs and a widely used model organism in experimental and theoretical ecology. Although its central role in applied and basic research in aquatic ecology is obvious, there are still fundamental problems in modelling the observed dynamics of Daphnia (for details see chapter 2). Therefore, a basic motivation of this work was to use scientific results obtained in independently conducted research for developing a model that brings these results into context. Instead of following a &quot;problem-oriented&quot; paradigm applicable to a single, well defined problem or scientific hypothesis, the underlying concept of the emerging model system was considered to be &quot;species-oriented&quot;. Thus, various relevant processes are included into the framework in order to simulate the dynamics of daphnids displayed on different levels of biological organization. To facilitate its application to various problems in ecological research on the genus Daphnia, the model system fulfills the following three important properties: (1) model outputs are thoroughly validated on experimental data in order to guarantee sound quantitative outputs of the model system (2) the system spans over different levels of biological organization with special emphasis laid upon the individual level and the population level (3) the model´s architecture follows a nested design with a defined individual level model that is integrated into a population level model The whole model system is able to describe an individual´s development over time on basis of physiological properties of the organism and, furthermore, how these individual level processes interact with the dynamics on the population level. Due to its nested design, applications of separate submodels (e.g. the individual-level model) are possible

Orientador: Fabio Cesar Gozzo
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Quimica
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Resumo: A espectrometria de massas (MS) desempenha um papel fundamental na proteômica, pois permite a identificação de proteínas, seqüenciamento de peptídeos, determinação de modificações pós-traducionais e análise quantitativa de expressão. Além das análises envolvendo a estrutura primária, há um grande interesse em se aplicar MS para análise de estruturas superiores (terciárias e quaternárias) de proteínas e uma das abordagens promissoras nesta área é a MS acoplada à ligação cruzada. Nesta abordagem, um reagente bifuncional liga covalentemente resíduos de aminoácidos espacialmente próximos e a distância máxima entre esses resíduos é dado pelo tamanho do agente de ligação cruzada (ALC). Nesse trabalho avaliou-se a extensão e exatidão das distâncias interresíduos tanto por simulações de dinâmica molecular quanto por experimentos de MS. As faixas de distâncias calculadas mostram que há sempre uma distância mínima entre resíduos ao qual o ALC pode se ligar, além de determinar o valor máximo para cada um dos ALC estudados (DSG, DSS e DSSeb). Os dados experimentais com proteínas modelo (Ubiquitina, Citocromo C e Mioglobina) mostraram ainda que todos dos peptídeos que apresentavam ligações cruzadas estavam dentro da faixa de alcance determinadas pelas simulações de dinâmica molecular, confirmando a exatidão do método. Os novos valores de tamanho das moléculas de ALC estudados podem agora ser utilizados para a determinação de estruturas superiores de proteínas através da técnica de MS acoplada a ligação cruzada
Abstract: Mass spectrometry (MS) plays a key role in proteomics because it allows the identification of proteins, peptide sequencing, determination of post-translational modifications and quantitative expression analysis. There is a great interest in using MS to perform analysis beyond the primary structure, i. e. tertiary and quaternary structures, and one of the most promising approaches in this filed is MS coupled to cross-linking technique. In this approach, a bifunctional reagent covalently binds amino acid residues that are close in space and the maximum distance between these residues is given by the arm length of the cross-linking agent. In this study we evaluated the extent and accuracy of the inter-residues distances by both molecular dynamics simulations and MS experiments. Simulated distance ranges showed that there is a minimum distance between residues to which the reagent can bind and a maximum value for each of the studied reagents (DSG, DSS and DSSeb). The experimental data from model proteins (Ubiquitin, Cytochrome C and Myoglobin) also showed that all the detected modified peptides were within the ranges determined by the molecular dynamics simulations, confirming the accuracy of the method. The new space arm length values of the reagent molecules can now be used for the determination of proteins higher structures by the MS coupled to cross-linking technique
Mestrado
Quimica Organica
Mestre em Química